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2  structures 95  species 0  interactions 260  sequences 4  architectures

Family: Amidase02_C (PF12123)

Summary: N-acetylmuramoyl-l-alanine amidase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "N-acetylmuramoyl-L-alanine amidase". More...

N-acetylmuramoyl-L-alanine amidase Edit Wikipedia article

N-acetylmuramoyl-L-alanine amidase
Identifiers
EC number 3.5.1.28
CAS number 9013-25-6
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
Amidase_2
PDB 1sk4 EBI.jpg
crystal structure of the c-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein ialpha
Identifiers
Symbol Amidase_2
Pfam PF01510
InterPro IPR002502
SCOP 1lba
SUPERFAMILY 1lba
OPM superfamily 438
OPM protein 1sk4
Amidase_3
PDB 1jwq EBI.jpg
structure of the catalytic domain of cwlv, n-acetylmuramoyl-l-alanine amidase from bacillus(paenibacillus) polymyxa var.colistinus
Identifiers
Symbol Amidase_3
Pfam PF01520
Pfam clan CL0035
InterPro IPR002508
SCOP 1jwq
SUPERFAMILY 1jwq
Amidase_5
Identifiers
Symbol Amidase_5
Pfam PF05382
Pfam clan CL0125
InterPro IPR008044
Amidase02_C
Identifiers
Symbol Amidase02_C
Pfam PF12123
InterPro IPR021976

In enzymology, a N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) is an enzyme that catalyzes a chemical reaction that cleaves the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.

This enzyme belongs to the family of hydrolases, specifically those acting on carbon-nitrogen bonds other than peptide bonds in linear amides. The systematic name of this enzyme class is peptidoglycan amidohydrolase. Other names in common use include acetylmuramyl-L-alanine amidase, N-acetylmuramyl-L-alanine amidase, N-acylmuramyl-L-alanine amidase, acetylmuramoyl-alanine amidase, N-acetylmuramic acid L-alanine amidase, acetylmuramyl-alanine amidase, N-acetylmuramylalanine amidase, N-acetylmuramoyl-L-alanine amidase type I, and N-acetylmuramoyl-L-alanine amidase type II. This enzyme participates in peptidoglycan biosynthesis. Autolysins and some phage lysins are examples of N-acetylmuramoyl-L-alanine amidases.

See also[edit]

References[edit]

  • Campbell JN; Dierickx, L; Coyette, J; Leyh-Bouille, M; Guinand, M; Campbell, JN (1969). "An improved technique for the preparation of Streptomyces peptidases and N-acetylmuramyl-l-alanine amidase active on bacterial wall peptidoglycans". Biochemistry. 8 (1): 213–22. doi:10.1021/bi00829a031. PMID 5777325. 
  • Herbold DR, Glaser L (1975). "Interaction of N-acetylmuramic acid L-alanine amidase with cell wall polymers". J. Biol. Chem. 250 (18): 7231–8. PMID 809432. 
  • Herbold DR, Glaser L (1975). "Bacillus subtilis N-acetylmuramic acid L-alanine amidase". J. Biol. Chem. 250 (5): 1676–82. PMID 803507. 
  • Ward JB, Curtis CA, Taylor C, Buxton RS (1982). "Purification and characterization of two phage PBSX-induced lytic enzymes of Bacillus subtilis 168: an N-acetylmuramoyl-L-alanine amidase and an N-acetylmuramidase". J. Gen. Microbiol. 128 (6): 1171–8. PMID 6126517. 

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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.

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This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code EC:3.5.1.28. This domain is the C terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021976

This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.

Domain organisation

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

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Alignments

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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
(16)
Full
(260)
Representative proteomes NCBI
(151)
Meta
(0)
RP15
(0)
RP35
(4)
RP55
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RP75
(9)
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  Seed
(16)
Full
(260)
Representative proteomes NCBI
(151)
Meta
(0)
RP15
(0)
RP35
(4)
RP55
(4)
RP75
(9)
Alignment:
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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
(16)
Full
(260)
Representative proteomes NCBI
(151)
Meta
(0)
RP15
(0)
RP35
(4)
RP55
(4)
RP75
(9)
Raw Stockholm Download   Download     Download   Download   Download   Download    
Gzipped 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: pdb_2ir9
Previous IDs: none
Type: Domain
Author: Mistry J, Gavin OL
Number in seed: 16
Number in full: 260
Average length of the domain: 44.60 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 18.36 %

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 21.4 21.4
Trusted cut-off 21.7 26.4
Noise cut-off 21.2 21.3
Model length: 45
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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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 Amidase02_C domain has been found. There are 2 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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