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302  structures 3791  species 3  interactions 13942  sequences 160  architectures

Family: Beta-lactamase (PF00144)

Summary: Beta-lactamase

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Beta-lactamase Edit Wikipedia article

Beta-lactamase
PDB 1bsg EBI.jpg
Structure of a Streptomyces albus beta-lactamase
Identifiers
Symbol β-lactamase domain
Pfam PF00144
Pfam clan CL0013
InterPro IPR001466
PROSITE PS00146
SCOP 56601
SUPERFAMILY 56601
β-lactamase
Lactamase Application V.1.svg
Action of β-lactamase and decarboxylation of the intermediate
Identifiers
EC number 3.5.2.6
CAS number 9073-60-3
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Core structure of penicillins (top) and cephalosporins (bottom). β-lactam ring in red.
Escherichia coli bacteria on the right are sensitive to two beta-lactam antibiotics, and do not grow in the semi-circular regions surrounding the antibiotics. E. coli bacteria on the left are resistant to beta-lactam antibiotics, and grow next to one antibiotic (bottom) and are less inhibited by another antibiotic (top).

Beta-lactamases are enzymes (EC 3.5.2.6) produced by some bacteria that provide resistance to beta-lactam antibiotics like penicillins, cephamycins, and carbapenems (ertapenem), although carbapenems are relatively resistant to beta-lactamase. Beta-lactamase provides antibiotic resistance by breaking the antibiotics' structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a beta-lactam. Through hydrolysis, the lactamase enzyme breaks the β-lactam ring open, deactivating the molecule's antibacterial properties.

Beta-lactam antibiotics are typically used to treat a broad spectrum of Gram-positive and Gram-negative bacteria.

Beta-lactamases produced by Gram-negative organisms are usually secreted, especially when antibiotics are present in the environment.[1]

Structure[edit]

The structure of a Streptomyces β-lactamase is given by 1BSG.

Penicillinase[edit]

Penicillinase is a specific type of β-lactamase, showing specificity for penicillins, again by hydrolysing the beta-lactam ring. Molecular weights of the various penicillinases tend to cluster near 50 kiloDaltons.

Penicillinase was the first β-lactamase to be identified: It was first isolated by Abraham and Chain in 1940 from Gram-negative E. coli even before penicillin entered clinical use,[2] but penicillinase production quickly spread to bacteria that previously did not produce it or produced it only rarely. Penicillinase-resistant beta-lactams such as methicillin were developed, but there is now widespread resistance to even these.

Classification[edit]

Functional classification[edit]

The following functional classification for beta lactamases has been proposed:[3]

Group 1[edit]

CEPHALOSPORINASE, Molecular Class C (not inhibited by clavulanic acid)
Group 1 are cephalosporinases not inhibited by clavulanic acid, belonging to the molecular class C

Group 2[edit]

Group 2 are penicillinases, cephalosporinases, or both inhibited by clavulanic acid, corresponding to the molecular classes A and D reflecting the original TEM and SHV genes. Additionally, many class A TEM β-lactamases are inhibited by Beta-lactamase inhibitor protein (BLIP). Because of the increasing number of TEM- and SHV-derived β-lactamases, they were divided into two subclasses, 2a and 2b.

GROUP 2a
PENICILLINASE, Molecular Class A
The 2a subgroup contains just penicillinases.
GROUP 2b
BROAD-SPECTRUM, Molecular Class A
2b Opposite to 2a , 2b are broad-spectrum β-lactamases, meaning that they are capable of inactivating penicillins and cephalosporins at the same rate. Furthermore, new subgroups were segregated from subgroup 2b:
GROUP 2be
EXTENDED-SPECTRUM, Molecular Class A
Subgroup 2be, with the letter "e" for extended spectrum of activity, represents the ESBLs, which are capable of inactivating third-generation cephalosporins (ceftazidime, cefotaxime, and cefpodoxime) as well as monobactams (aztreonam)
GROUP 2br
INHIBITOR-RESISTANT, Molecular Class A (diminished inhibition by clavulanic acid)
The 2br enzymes, with the letter "r" denoting reduced binding to clavulanic acid and sulbactam, are also called inhibitor-resistant TEM-derivative enzymes; nevertheless, they are commonly still susceptible to tazobactam, except where an amino acid replacement exists at position met69.
GROUP 2c
CARBENICILLINASE, Molecular Class A
Latersubgroup 2c was segregated from group 2 because these enzymes inactivate carbenicillin more than benzylpenicillin, with some effect on cloxacillin.
GROUP 2d
CLOXACILANASE, Molecular Class D or A
Subgroup 2d enzymes inactivate cloxacillin more than benzylpenicillin, with some activity against carbenicillin; these enzymes are poorly inhibited by clavulanic acid, and some of them are ESBLs
the correct term is "OXACILLINASE". These enzymes are able to inactivate the oxazolylpenicillins like oxacillin, cloxacillin, dicloxacillin. The enzymes belong to the molecular class D not molecular class A.
GROUP 2e
CEPHALOSPORINASE, Molecular Class A
Subgroup 2e enzymes are cephalosporinases that can also hydrolyse monobactams, and they are inhibited by clavulanic acid
GROUP 2f
CARBAPENEMASE, Molecular Class A
Subgroup 2f was added because these are serine-based carbapenemases, in contrast to the zinc-based carbapenemases included in group 3

Group 3[edit]

METALLOENZYME, Molecular Class B (not inhibited by clavulanic acid)
Group 3 are the zinc-based or metallo {beta}-lactamases, corresponding to the molecular class B, which are the only enzymes acting by the metal ion zinc, as discussed above. Metallo B-lactamases are able to hydrolyse penicillins, cephalosporins, and carbapenems. Thus, carbapenems are inhibited by both group 2f (serine-based mechanism) and group 3 (zinc-based mechanism)

Group 4[edit]

PENICILLINASE, No Molecular Class (not inhibited by clavulanic acid)
Group 4 are penicillinases that are not inhibited by clavulanic acid, and they do not yet have a corresponding molecular class.

Molecular classification[edit]

The molecular classification of β-lactamases is based on the nucleotide and amino acid sequences in these enzymes. To date, four classes are recognised (A-D), correlating with the functional classification. Classes A, C, and D act by a serine-based mechanism, whereas class B or metallo-β-lactamases need zinc for their action[4]

"Penicillinase" was discovered in 1940 and renamed Beta-lactamase when the structure of the Beta-lactam ring was finally elucidated.

Resistance in Gram-negative bacteria[edit]

Among Gram-negative bacteria, the emergence of resistance to expanded-spectrum cephalosporins has been a major concern. It appeared initially in a limited number of bacterial species (E. cloacae, C. freundii, S. marcescens, and P. aeruginosa ) that could mutate to hyperproduce their chromosomal class C β-lactamase. A few years later, resistance appeared in bacterial species not naturally producing AmpC enzymes (K. pneumoniae, Salmonella spp., P. mirabilis) due to the production of TEM- or SHV-type ESBLs. Characteristically, such resistance has included oxyimino- (for example ceftizoxime, cefotaxime, ceftriaxone, and ceftazidime, as well as the oxyimino-monobactam aztreonam), but not 7-alpha-methoxy-cephalosporins (cephamycins); in other words, (cefoxitin and cefotetan) have been blocked by inhibitors such as clavulanate, sulbactam, or tazobactam, and did not involve carbapenems. Chromosomal-mediated AmpC β-lactamases represent a new threat, since they confer resistance to 7-alpha-methoxy-cephalosporins (cephamycins) such as cefoxitin or cefotetan are not affected by commercially available β-lactamase inhibitors, and can, in strains with loss of outer membrane porins, provide resistance to carbapenems.[5]

Extended-spectrum beta-lactamase (ESBL)[edit]

Members of the family Enterobacteriaceae commonly express plasmid-encoded β-lactamases (e.g., TEM-1, TEM-2, and SHV-1). which confer resistance to penicillins but not to expanded-spectrum cephalosporins. In the mid-1980s, a new group of enzymes, the extended-spectrum b-lactamases (ESBLs), was detected (first detected in 1979).[6] ESBLs are beta-lactamases that hydrolyze extended-spectrum cephalosporins with an oxyimino side chain. These cephalosporins include cefotaxime, ceftriaxone, and ceftazidime, as well as the oxyimino-monobactam aztreonam. Thus ESBLs confer resistance to these antibiotics and related oxyimino-beta lactams. In typical circumstances, they derive from genes for TEM-1, TEM-2, or SHV-1 by mutations that alter the amino acid configuration around the active site of these β-lactamases. This extends the spectrum of β-lactam antibiotics susceptible to hydrolysis by these enzymes. An increasing number of ESBLs not of TEM or SHV lineage have recently been described.[7] The ESBLs are frequently plasmid encoded. Plasmids responsible for ESBL production frequently carry genes encoding resistance to other drug classes (for example, aminoglycosides). Therefore, antibiotic options in the treatment of ESBL-producing organisms are extremely limited. Carbapenems are the treatment of choice for serious infections due to ESBL-producing organisms, yet carbapenem-resistant isolates have recently been reported. ESBL-producing organisms may appear susceptible to some extended-spectrum cephalosporins. However, treatment with such antibiotics has been associated with high failure rates.

Types[edit]

TEM beta-lactamases (class A)[edit]

TEM-1 is the most commonly encountered beta-lactamase in Gram-negative bacteria. Up to 90% of ampicillin resistance in E. coli is due to the production of TEM-1.[8] Also responsible for the ampicillin and penicillin resistance that is seen in H. influenzae and N. gonorrhoeae in increasing numbers. Although TEM-type beta-lactamases are most often found in E. coli and K. pneumoniae, they are also found in other species of Gram-negative bacteria with increasing frequency. The amino acid substitutions responsible for the ESBL phenotype cluster around the active site of the enzyme and change its configuration, allowing access to oxyimino-beta-lactam substrates. Opening the active site to beta-lactam substrates also typically enhances the susceptibility of the enzyme to b-lactamase inhibitors, such as clavulanic acid. Single amino acid substitutions at positions 104, 164, 238, and 240 produce the ESBL phenotype, but ESBLs with the broadest spectrum usually have more than a single amino acid substitution. Based upon different combinations of changes, currently 140 TEM-type enzymes have been described. TEM-10, TEM-12, and TEM-26 are among the most common in the United States.[9][10][11]

SHV beta-lactamases (class A)[edit]

SHV-1 shares 68 percent of its amino acids with TEM-1 and has a similar overall structure. The SHV-1 beta-lactamase is most commonly found in K. pneumoniae and is responsible for up to 20% of the plasmid-mediated ampicillin resistance in this species. ESBLs in this family also have amino acid changes around the active site, most commonly at positions 238 or 238 and 240. More than 60 SHV varieties are known. SHV-5 and SHV-12 are among the most common.[9]

CTX-M beta-lactamases (class A)[edit]

These enzymes were named for their greater activity against cefotaxime than other oxyimino-beta-lactam substrates (e.g., ceftazidime, ceftriaxone, or cefepime). Rather than arising by mutation, they represent examples of plasmid acquisition of beta-lactamase genes normally found on the chromosome of Kluyvera species, a group of rarely pathogenic commensal organisms. These enzymes are not very closely related to TEM or SHV beta-lactamases in that they show only approximately 40% identity with these two commonly isolated beta-lactamases. More than 80 CTX-M enzymes are currently known. Despite their name, a few are more active on ceftazidime than cefotaxime. They have mainly been found in strains of Salmonella enterica serovar Typhimurium and E. coli, but have also been described in other species of Enterobacteriaceae and are the predominant ESBL type in parts of South America. (They are also seen in eastern Europe) CTX-M-14, CTX-M-3, and CTX-M-2 are the most widespread. CTX-M-15 is currently (2006) the most widespread type in E. coli the UK and is widely prevalent in the community.[12]

OXA beta-lactamases (class D)[edit]

OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d . The OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. While most ESBLs have been found in E. coli, K. pneumoniae, and other Enterobacteriaceae, the OXA-type ESBLs have been found mainly in P. aeruginosa. OXA-type ESBLs have been found mainly in Pseudomonas aeruginosa isolates from Turkey and France. The OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.

Others[edit]

Other plasmid-mediated ESBLs, such as PER, VEB, GES, and IBC beta-lactamases, have been described but are uncommon and have been found mainly in P. aeruginosa and at a limited number of geographic sites. PER-1 in isolates in Turkey, France, and Italy; VEB-1 and VEB-2 in strains from Southeast Asia; and GES-1, GES-2, and IBC-2 in isolates from South Africa, France, and Greece. PER-1 is also common in multiresistant acinetobacter species in Korea and Turkey. Some of these enzymes are found in Enterobacteriaceae as well, whereas other uncommon ESBLs (such as BES-1, IBC-1, SFO-1, and TLA-1) have been found only in Enterobacteriaceae.

Treatment[edit]

While ESBL-producing organisms were previously associated with hospitals and institutional care, these organisms are now increasingly found in the community. CTX-M-15-positive E. coli are a cause of community-acquired urinary infections in the UK,[12] and tend to be resistant to all oral β-lactam antibiotics, as well as quinolones and sulfonamides. Treatment options may include nitrofurantoin, fosfomycin, mecillinam and chloramphenicol. In desperation, once-daily ertapenem or gentamicin injections may also be used.

Inhibitor-resistant β-lactamases[edit]

Although the inhibitor-resistant β-lactamases are not ESBLs, they are often discussed with ESBLs because they are also derivatives of the classical TEM- or SHV-type enzymes. These enzymes were at first given the designation IRT for inhibitor-resistant TEM β-lactamase; however, all have subsequently been renamed with numerical TEM designations. There are at least 19 distinct inhibitor-resistant TEM β-lactamases. Inhibitor-resistant TEM β-lactamases have been found mainly in clinical isolates of E. coli, but also some strains of K. pneumoniae, Klebsiella oxytoca, P. mirabilis, and Citrobacter freundii. Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam—lactamase inhibitor combinations of amoxicillin-clavulanate (co-amoxiclav), ticarcillin-clavulanate (co-ticarclav), and ampicillin/sulbactam, they normally remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin/tazobactam, although resistance has been described. This is no longer a primarily European epidemiology, it is found in northern parts of America often and should be tested for with complex UTI's.[10]

AmpC-type β-lactamases (Class C)[edit]

AmpC type β-lactamases are commonly isolated from extended-spectrum cephalosporin-resistant Gram-negative bacteria. AmpC β-lactamases (also termed class C or group 1) are typically encoded on the chromosome of many Gram-negative bacteria including Citrobacter, Serratia and Enterobacter species where its expression is usually inducible; it may also occur on Escherichia coli but is not usually inducible, although it can be hyperexpressed. AmpC type β-lactamases may also be carried on plasmids.[5] AmpC β-lactamases, in contrast to ESBLs, hydrolyse broad and extended-spectrum cephalosporins (cephamycins as well as to oxyimino-β-lactams) but are not inhibited by β-lactamase inhibitors such as clavulanic acid.

Carbapenemases[edit]

Carbapenems are famously stable to AmpC β-lactamases and extended-spectrum-β-lactamases. Carbapenemases are a diverse group of β-lactamases that are active not only against the oxyimino-cephalosporins and cephamycins but also against the carbapenems. Aztreonam is stable to the metallo-β-lactamases, but many IMP and VIM producers are resistant, owing to other mechanisms. Carbapenemases were formerly believed to derive only from classes A, B, and D, but a class C carbapenemase has been described.

IMP-type carbapenemases (metallo-β-lactamases) (Class B)[edit]

Plasmid-mediated IMP-type carbapenemases, 17 varieties of which are currently known, became established in Japan in the 1990s both in enteric Gram-negative organisms and in Pseudomonas and Acinetobacter species. IMP enzymes spread slowly to other countries in the Far East, were reported from Europe in 1997, and have been found in Canada and Brazil.

VIM (Verona integron-encoded metallo-β-lactamase) (Class B)[edit]

A second growing family of carbapenemases, the VIM family, was reported from Italy in 1999 and now includes 10 members, which have a wide geographic distribution in Europe, South America, and the Far East and have been found in the United States. VIM-1 was discovered in P. aeruginosa in Italy in 1996; since then, VIM-2 - now the predominant variant - was found repeatedly in Europe and the Far East; VIM-3 and -4 are minor variants of VIM-2 and -1, respectively. VIM enzymes occur mostly in P. aeruginosa, also P. putida and, very rarely, Enterobacteriaceae.

Amino acid sequence diversity is up to 10% in the VIM family, 15% in the IMP family, and 70% between VIM and IMP. Enzymes of both the families, nevertheless, are similar. Both are integron-associated, sometimes within plasmids. Both hydrolyse all β-lactams except monobactams, and evade all β-lactam inhibitors.

OXA (oxacillinase) group of β-lactamases (Class D)[edit]

The OXA group of β-lactamases occur mainly in Acinetobacter species and are divided into two clusters. OXA carbapenemases hydrolyse carbapenems very slowly in vitro, and the high MICs seen for some Acinetobacter hosts (>64 mg/L) may reflect secondary mechanisms. They are sometimes augmented in clinical isolates by additional resistance mechanisms, such as impermeability or efflux. OXA carbapenemases also tend to have a reduced hydrolytic efficiency towards penicillins and cephalosporins.[13]

KPC (K. pneumoniae carbapenemase) (Class A)[edit]

A few class A enzymes, most noted the plasmid-mediated KPC enzymes, are effective carbapenemases as well. Ten variants, KPC-2 through KPC-11 are known, and they are distinguished by one or two amino acid substitutions (KPC-1 was re-sequenced in 2008 and found to be 100% homologous to published sequences of KPC-2). KPC-1 was found in North Carolina, KPC-2 in Baltimore and KPC-3 in New York. They have only 45% homology with SME and NMC/IMI enzymes and, unlike them, can be encoded by self-transmissible plasmids.

The class A Klebsiella pneumoniae carbapenemase (KPC) is currently the most common carbapenemase, which was first detected in North Carolina, US, in 1996 and has since spread worldwide.[14] A later publication indicated that Enterobacteriaceae that produce KPC were becoming common in the United States.[15]

CMY (Class C)[edit]

The first class C carbapenemase was described in 2006 and was isolated from a virulent strain of Enterobacter aerogenes.[16] It is carried on a plasmid, pYMG-1, and is therefore transmissible to other bacterial strains.[17]

SME, IMI, NMC and CcrA[edit]

In general, these are of little clinical significance.

CcrA (CfiA). Its gene occurs in c. 1-3% of B. fragilis isolates, but fewer produce the enzyme since expression demands appropriate migration of an insertion sequence. CcrA was known before imipenem was introduced, and producers have shown little subsequent increase.

NDM-1 (New Delhi metallo-β-lactamase) (Class B)[edit]

Originally described from New Delhi in 2009, this gene is now widespread in Escherichia coli and Klebsiella pneumoniae from India and Pakistan. As of mid-2010, NDM-1 carrying bacteria have been introduced to other countries (including the United States and UK), most probably due to the large number of tourists travelling the globe, who may have picked up the strain from the environment, as strains containing the NDM-1 gene have been found in environmental samples in India.[18]

Treatment of ESBL/AmpC/carbapenemases[edit]

General overview[edit]

In general, an isolate is suspected to be an ESBL producer when it shows in vitro susceptibility to the second-generation cephalosporins (cefoxitin, cefotetan) but resistance to the third-generation cephalosporins and to aztreonam. Moreover, one should suspect these strains when treatment with these agents for Gram-negative infections fails despite reported in vitro susceptibility. Once an ESBL-producing strain is detected, the laboratory should report it as "resistant" to all penicillins, cephalosporins, and aztreonam, even if it is tested (in vitro) as susceptible.[citation needed] Associated resistance to aminoglycosides and trimethoprim-sulfamethoxazole, as well as high frequency of co-existence of fluoroquinolone resistance, creates problems. Beta-lactamase inhibitors such as clavulanate, sulbactam, and tazobactam in vitro inhibit most ESBLs, but the clinical effectiveness of beta-lactam/beta-lactamase inhibitor combinations cannot be relied on consistently for therapy. Cephamycins (cefoxitin and cefotetan) are not hydrolyzed by majority of ESBLs, but are hydrolyzed by associated AmpC-type β-lactamase. Also, β-lactam/β-lactamase inhibitor combinations may not be effective against organisms that produce AmpC-type β-lactamase. Sometimes these strains decrease the expression of outer membrane proteins, rendering them resistant to cephamycins. In vivo studies have yielded mixed results against ESBL-producing K. pneumoniae. (Cefepime, a fourth-generation cephalosporin, has demonstrated in vitro stability in the presence of many ESBL/AmpC strains.) Currently, carbapenems are, in general, regarded as the preferred agent for treatment of infections due to ESBL-producing organisms. Carbapenems are resistant to ESBL-mediated hydrolysis and exhibit excellent in vitro activity against strains of Enterobacteriaceae expressing ESBLs.[citation needed]

According to genes[edit]

ESBLs[edit]

Strains producing only ESBLs are susceptible to cephamycins and carbapenems in vitro and show little if any inoculum effect with these agents.

For organisms producing TEM and SHV type ESBLs, apparent in vitro sensitivity to cefepime and to piperacillin/tazobactam is common, but both drugs show an inoculum effect, with diminished susceptibility as the size of the inoculum is increased from 105to 107organisms.

Strains with some CTX-M–type and OXA-type ESBLs are resistant to cefepime on testing, despite the use of a standard inoculum.

Inhibitor-Resistant β-Lactamases[edit]

Although the inhibitor-resistant TEM variants are resistant to inhibition by clavulanic acid and sulbactam, thereby showing clinical resistance to the beta-lactam—lactamase inhibitor combinations of amoxicillin-clavulanate (Co-amoxiclav), ticarcillin-clavulanate, and ampicillin/sulbactam, they remain susceptible to inhibition by tazobactam and subsequently the combination of piperacillin/tazobactam.

AmpC[edit]

AmpC-producing strains are typically resistant to oxyimino-beta lactams and to cephamycins and are susceptible to carbapenems; however, diminished porin expression can make such a strain carbapenem-resistant as well.

Carbapenemases[edit]

Strains with IMP-, VIM-, and OXA-type carbapenemases usually remain susceptible. Resistance to non–b-lactam antibiotics is common in strains making any of these enzymes, such that alternative options for non–b-lactam therapy need to be determined by direct susceptibility testing. Resistance to fluoroquinolones and aminoglycosides is especially high.

According to species[edit]

Escherichia coli or Klebsiella[edit]

For infections caused by ESBL-producing Escherichia coli or Klebsiella species, treatment with imipenem or meropenem has been associated with the best outcomes in terms of survival and bacteriologic clearance. Cefepime and piperacillin/tazobactam have been less successful. Ceftriaxone, cefotaxime, and ceftazidime have failed even more often, despite the organism's susceptibility to the antibiotic in vitro. Several reports have documented failure of cephamycin therapy as a result of resistance due to porin loss. Some patients have responded to aminoglycoside or quinolone therapy, but, in a recent comparison of ciprofloxacin and imipenem for bacteremia involving an ESBL-producing K. pneumoniae, imipenem produced the better outcome

Pseudomonas aeruginosa[edit]

There have been few clinical studies to define the optimal therapy for infections caused by ESBL producing Pseudomonas aeruginosa strains.

Detection[edit]

Beta-lactamase enzymatic activity can be detected using nitrocefin, a chromogenic cephalosporin substrate which changes color from yellow to red upon beta-lactamase mediated hydrolysis.[19]

Evolution[edit]

Betalactamases are ancient bacterial enzymes. The class B betalactamases (the metallo-beta-lactamases) are divided into three subclasses: B1, B2 and B3. Subclass B1+B2 evolved about 1,000 million years ago) ago and subclass B3 evolved before the divergence of the Gram positive and Gram negative eubacteria about 2,000 million years ago.[20]

The other three groups are serine enzymes that show little homology to each other. Structural studies have shown that group A and D are sister taxa and that group C diverged before A and D.[21] These serine based enzymes like the group B betalactamases are of ancient origin having evolved about 2,000 million years ago.[22]

The OXA group (in class D) in particular evolved on chromosomes and moved to plasmids on at least two separate occasions.[23]

See also[edit]

References[edit]

  1. ^ Neu HC (June 1969). "Effect of beta-lactamase location in Escherichia coli on penicillin synergy". Appl Microbiol 17 (6): 783–6. PMC 377810. PMID 4894721. 
  2. ^ Abraham EP, Chain E (1940). "An enzyme from bacteria able to destroy penicillin". Nature 46 (3713): 837–837. doi:10.1038/146837a0. 
  3. ^ Bush K, Jacoby GA, Medeiros AA (June 1995). "A functional classification scheme for beta-lactamases and its correlation with molecular structure". Antimicrob. Agents Chemother. 39 (6): 1211–33. doi:10.1128/AAC.39.6.1211. PMC 162717. PMID 7574506. 
  4. ^ Ambler RP (May 1980). "The structure of beta-lactamases". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 289 (1036): 321–31. doi:10.1098/rstb.1980.0049. PMID 6109327. 
  5. ^ a b Philippon A, Arlet G, Jacoby GA (January 2002). "Plasmid-determined AmpC-type beta-lactamases". Antimicrob. Agents Chemother. 46 (1): 1–11. doi:10.1128/AAC.46.1.1-11.2002. PMC 126993. PMID 11751104. 
  6. ^ Sanders CC, Sanders WE (June 1979). "Emergence of resistance to cefamandole: possible role of cefoxitin-inducible beta-lactamases". Antimicrob. Agents Chemother. 15 (6): 792–7. doi:10.1128/AAC.15.6.792. PMC 352760. PMID 314270. 
  7. ^ Emery CL, Weymouth LA (August 1997). "Detection and clinical significance of extended-spectrum beta-lactamases in a tertiary-care medical center". J. Clin. Microbiol. 35 (8): 2061–7. PMC 229903. PMID 9230382. 
  8. ^ Cooksey R, Swenson J, Clark N, Gay E, Thornsberry C (May 1990). "Patterns and mechanisms of beta-lactam resistance among isolates of Escherichia coli from hospitals in the United States". Antimicrob. Agents Chemother. 34 (5): 739–45. doi:10.1128/AAC.34.5.739. PMC 171683. PMID 2193616. 
  9. ^ a b Paterson DL, Hujer KM, Hujer AM, Yeiser B, Bonomo MD, Rice LB, Bonomo RA (November 2003). "Extended-spectrum beta-lactamases in Klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of SHV- and CTX-M-type beta-lactamases". Antimicrob. Agents Chemother. 47 (11): 3554–60. doi:10.1128/AAC.47.11.3554-3560.2003. PMC 253771. PMID 14576117. 
  10. ^ a b Bradford PA (October 2001). "Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat". Clin. Microbiol. Rev. 14 (4): 933–51, table of contents. doi:10.1128/CMR.14.4.933-951.2001. PMC 89009. PMID 11585791. 
  11. ^ Jacoby GA, Munoz-Price LS (January 2005). "The new beta-lactamases". N. Engl. J. Med. 352 (4): 380–91. doi:10.1056/NEJMra041359. PMID 15673804. 
  12. ^ a b Woodford N, Ward E, Kaufmann ME, et al.. "Molecular characterisation of Escherichia coli isolates producing CTX-M-15 extended-spectrum β-lactamase (ESBL) in the United Kingdom" (PDF). Health Protection Agency. Retrieved 2006-11-19. 
  13. ^ Santillana E, Beceiro A, Bou G, Romero A (March 2007). "Crystal structure of the carbapenemase OXA-24 reveals insights into the mechanism of carbapenem hydrolysis". Proc. Natl. Acad. Sci. U.S.A. 104 (13): 5354–9. doi:10.1073/pnas.0607557104. PMC 1838445. PMID 17374723. 
  14. ^ Nordmann P, Cuzon G, Naas T (April 2009). "The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria". Lancet Infect Dis 9 (4): 228–36. doi:10.1016/S1473-3099(09)70054-4. PMID 19324295. 
  15. ^ Cuzon G, Naas T, Nordmann P (February 2010). "[KPC carbapenemases: what is at stake in clinical microbiology?]". Pathol. Biol. (in French) 58 (1): 39–45. doi:10.1016/j.patbio.2009.07.026. PMID 19854586. 
  16. ^ Kim JY, Jung HI, An YJ, Lee JH, Kim SJ, Jeong SH, Lee KJ, Suh PG, Lee HS, Lee SH, Cha SS (May 2006). "Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase". Mol. Microbiol. 60 (4): 907–16. doi:10.1111/j.1365-2958.2006.05146.x. PMID 16677302. 
  17. ^ Lee JH, Jung HI, Jung JH, Park JS, Ahn JB, Jeong SH, Jeong BC, Lee JH, Lee SH (2004). "Dissemination of transferable AmpC-type beta-lactamase (CMY-10) in a Korean hospital". Microb. Drug Resist. 10 (3): 224–30. doi:10.1089/mdr.2004.10.224. PMID 15383166. 
  18. ^ Walsh TR, Weeks J, Livermore DM, Toleman MA (May 2011). "Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study". Lancet Infect Dis 11 (5): 355–62. doi:10.1016/S1473-3099(11)70059-7. PMID 21478057. 
  19. ^ O'Callaghan CH, Morris A, Kirby SM, Shingler AH (April 1972). "Novel method for detection of beta-lactamases by using a chromogenic cephalosporin substrate". Antimicrob. Agents Chemother. 1 (4): 283–8. doi:10.1128/AAC.1.4.283. PMC 444209. PMID 4208895. 
  20. ^ Hall BG, Salipante SJ, Barlow M (July 2004). "Independent origins of subgroup Bl + B2 and subgroup B3 metallo-beta-lactamases". J. Mol. Evol. 59 (1): 133–41. doi:10.1007/s00239-003-2572-9. PMID 15383916. 
  21. ^ Hall BG, Barlow M (September 2003). "Structure-based phylogenies of the serine beta-lactamases". J. Mol. Evol. 57 (3): 255–60. doi:10.1007/s00239-003-2473-y. PMID 14629035. 
  22. ^ Hall BG, Barlow M (April 2004). "Evolution of the serine beta-lactamases: past, present and future". Drug Resist. Updat. 7 (2): 111–23. doi:10.1016/j.drup.2004.02.003. PMID 15158767. 
  23. ^ Barlow M, Hall BG (September 2002). "Phylogenetic analysis shows that the OXA beta-lactamase genes have been on plasmids for millions of years". J. Mol. Evol. 55 (3): 314–21. doi:10.1007/s00239-002-2328-y. PMID 12187384. 

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Beta-lactamase Provide feedback

This family appears to be distantly related to PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001466

This entry represents the serine beta-lactamase-like superfamily. It is a group of diverse group of sequences that includes D-alanyl-D-alanine carboxypeptidase B, aminopeptidase (DmpB), alkaline D-peptidase, animal D-Ala-D-Ala carboxypeptidase homologues and the class A and C beta-lactamases and eukaryotic beta-lactamase homologues which are variously described as: transesterases, non-ribosomal peptide synthetases and hypothetical proteins. Many are serine peptidases belonging to MEROPS peptidase families S11 (D-Ala-D-Ala carboxypeptidase A family) and S12 (D-Ala-D-Ala carboxypeptidase B family, clan SE). The beta-lactamases are classified as both S11 and S12 non-peptidase homologues; these either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.

Beta-lactamase catalyses the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins [PUBMED:1856867]. There are four groups, classed A, B, C and D according to sequence, substrate specificity, and kinetic behaviour: class A (penicillinase-type) is the most common [PUBMED:1856867]. The genes for class A beta-lactamases are widely distributed in bacteria, frequently located on transmissible plasmids in Gram-negative organisms, although an equivalent chromosomal gene has been found in a few species [PUBMED:2788410].

Class A, C and D beta-lactamases are serine-utilising hydrolases - class B enzymes utilise a catalytic zinc centre instead. The 3 classes of serine beta-lactamase are evolutionarily related and belong to a superfamily that also includes DD-peptidases and other penicillin-binding proteins [PUBMED:3128280]. All these proteins contain an S-x-x-K motif, the Ser being the active site residue. Although clearly related, however, the sequences of the 3 classes of serine beta-lactamases vary considerably outside the active site.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Beta-lactamase (CL0013), which has the following description:

This superfamily contains proteins that have a beta-lactamase fold. This includes beta-lactamases as well as Dala-Dala carboxypeptidases and glutaminases.

The clan contains the following 7 members:

Beta-lactamase Beta-lactamase2 DAP_B Glutaminase Peptidase_S11 Peptidase_S13 Transpeptidase

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(127)
Full
(13942)
Representative proteomes NCBI
(15232)
Meta
(5643)
RP15
(1339)
RP35
(2525)
RP55
(3318)
RP75
(3910)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(127)
Full
(13942)
Representative proteomes NCBI
(15232)
Meta
(5643)
RP15
(1339)
RP35
(2525)
RP55
(3318)
RP75
(3910)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(127)
Full
(13942)
Representative proteomes NCBI
(15232)
Meta
(5643)
RP15
(1339)
RP35
(2525)
RP55
(3318)
RP75
(3910)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite and Pfam-B_106 (Release 7.5)
Previous IDs: beta-lactamase;
Type: Domain
Author: Sonnhammer ELL, Bateman A
Number in seed: 127
Number in full: 13942
Average length of the domain: 321.50 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 75.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.9 19.9
Trusted cut-off 19.9 19.9
Noise cut-off 19.8 19.8
Model length: 330
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 3 interactions for this family. More...

DAP_B Beta-lactamase DAP_C

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Beta-lactamase domain has been found. There are 302 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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