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45  structures 4283  species 2  interactions 4669  sequences 21  architectures

Family: DHQ_synthase (PF01761)

Summary: 3-dehydroquinate synthase

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This is the Wikipedia entry entitled "3-dehydroquinate synthase". More...

3-dehydroquinate synthase Edit Wikipedia article

3-dehydroquinate synthase
3-dehydroquinate synthase 3CLH.png
Ribbon representation of the Helicobacter pylori 3-dehydroquinate synthase.[1]
Identifiers
EC number 4.2.3.4
CAS number 37211-77-1
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
3-dehydroquinate synthase
Identifiers
Symbol DHQ_synthase
Pfam PF01761
InterPro IPR002658
SCOP 1dqs
SUPERFAMILY 1dqs

In enzymology, a 3-dehydroquinate synthase (EC 4.2.3.4) is an enzyme that catalyzes the chemical reaction

3-deoxy-arabino-heptulosonate 7-phosphate \rightleftharpoons 3-dehydroquinate + phosphate

Hence, this enzyme has one substrate, 3-deoxy-arabino-heptulosonate 7-phosphate, and two products, 3-dehydroquinate and phosphate. The protein uses NAD+ to catalyze the reaction.[2][3] This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids.

3-Dehydroquinate synthase belongs to the family of lyases, to be specific those carbon-oxygen lyases acting on phosphates. This enzyme participates in phenylalanine, tyrosine, and tryptophan biosynthesis. It employs one cofactor, cobalt.

The reaction catalyzed by 3-dehydroquinate synthase

Background[edit]

The shikimate pathway is composed of seven steps, each catalyzed by an enzyme. The shikimate pathway is responsible for producing the precursors for aromatic amino acids, which are essential to our diets because we cannot synthesize them in our bodies. Only plants, bacteria, and microbial eukaryotes are capable of producing aromatic amino acids. The pathway ultimately converts phosphoenolpyruvate and 4-erythrose phosphate into chorismate, the precursor to aromatic amino acids. 3-Dehydroquinate synthase is the enzyme that catalyzes reaction in the second step of this pathway. This second step of the reaction eliminates a phosphate from 3-deoxy-D-arabino-heptulosonate 7-phosphate, which results in 3-dehydroquinate. 3-Dehydroquinate synthase is a monomeric enzyme, and has a molecular weight of 39,000.[4] 3-dehydroquinate synthase is activated by inorganic phosphate, and requires NAD+ for activity, although the reaction in total is neutral when catalyzed by an enzyme.[4]

Function[edit]

3-Dehydroquinate synthase utilizes a complex multi-step mechanism that includes alcohol oxidation, phosphate b-elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation.[5] Dehydroquinate synthase requires NAD+ and a cobalt cofactor to catalyze the conversion of 3-deoxy-D-arabino-heptulosonate 7-phosphate into 3-dehydroquinate. In most bacteria, this enzyme has only one function. However, in some organisms, it forms a complex with other enzymes. This complex is known as the AROM complex. The AROM complex is a pentafunctional polypeptide, which contains enzymes that catalyze steps two, three, four, and five of the shikimate pathway.[5] In addition, dehydroquinate synthase is of particular interest because of its complicated activity relative to its small size.[5]

Applications[edit]

3-Dehydroquinate synthase catalyzes the second step in the shikimate pathway, which is essential for the production of aromatic amino acids in bacteria, plants, and fungi, but not mammals. This makes it an ideal target for new antimicrobial agents, anti-parasitic agents, and herbicides.[1] Other enzymes in the shikimate pathway have already been targeted and put to use as herbicides. Roundup, a common herbicide made by Monsanto, works by inhibiting another enzyme in the shikimate pathway. The shikimate pathway is an ideal choice for herbicides because this pathway does not exist in animals or people so people are not directly affected. Roundup uses an enzyme inhibitor, glyphosphate, to block one of the steps of the shikimate pathway. Glyphosate inhibits 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase), which ultimately blocks the production of aromatic amino acids, and, without aromatic amino acids, plants cannot survive. However, Monsanto developed a bacterial form of EPSP synthase that was not inhibited by Roundup. Monsanto introduced this gene into plants using agrobacterium and the result was a plant that was resistant to Roundup. This meant that all plants without the bacterial gene would die, leading a much higher degree of weed control.

This cartoon representation of 3-dehydroquinate synthase shows the arrangement of the secondary structure of the protein
3-dehydroquiante synthase interacting with its substrates NAD+, carbaphosphonate, and Zn2+, which are shown as spheres in this representation
This representation of 3-dehydroquinate synthase shows the surface of the enzyme, as well as the active site, which can be seen in the middle.

Nomenclature[edit]

The systematic name of this enzyme class is 3-deoxy-arabino-heptulonate-7-phosphate phosphate-lyase (cyclizing 3-dehydroquinate-forming). Other names in common use include 5-dehydroquinate synthase, 5-dehydroquinic acid synthetase, dehydroquinate synthase, 3-dehydroquinate synthetase, 3-deoxy-arabino-heptulosonate-7-phosphate phosphate-lyase, (cyclizing), and 3-deoxy-arabino-heptulonate-7-phosphate phosphate-lyase (cyclizing).

References[edit]

  1. ^ a b PDB 3CLH; Liu JS, Cheng WC, Wang HJ, Chen YC, Wang WC (2008). "Structure-based inhibitor discovery of Helicobacter pylori dehydroquinate synthase". Biochem. Biophys. Res. Commun. 373 (1): 1–7. doi:10.1016/j.bbrc.2008.05.070. PMID 18503755. ; rendered with MacPyMOL
  2. ^ Hawkins AR, Lamb HK (August 1995). "The molecular biology of multidomain proteins. Selected examples". Eur. J. Biochem. 232 (1): 7–18. doi:10.1111/j.1432-1033.1995.tb20775.x. PMID 7556173. 
  3. ^ Barten R, Meyer TF (April 1998). "Cloning and characterisation of the Neisseria gonorrhoeae aroB gene". Mol. Gen. Genet. 258 (1-2): 34–44. PMID 9613570. 
  4. ^ a b Herrmann KM, Weaver LM (June 1999). "The Shikimate Pathway". Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 473–503. doi:10.1146/annurev.arplant.50.1.473. PMID 15012217. 
  5. ^ a b c Negron L, Patchett ML, Parker EJ (2011). "Expression, Purification, and Characterisation of Dehydroquinate Synthase from Pyrococcus furiosus". Enzyme Res 2011: 134893. doi:10.4061/2011/134893. PMC 3092513. PMID 21603259. 

Further reading[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.

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The 3-dehydroquinate synthase EC:4.6.1.3 domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide P07547 [2]. 3-dehydroquinate (DHQ) synthase catalyses the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate [1]. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids.

Literature references

  1. Barten R, Meyer TF; , Mol Gen Genet 1998;258:34-44.: Cloning and characterisation of the Neisseria gonorrhoeae aroB gene. PUBMED:9613570 EPMC:9613570

  2. Hawkins AR, Lamb HK; , Eur J Biochem 1995;232:7-18.: The molecular biology of multidomain proteins. Selected examples. PUBMED:7556173 EPMC:7556173


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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Pfam Clan

This family is a member of clan DHQS (CL0224), which has the following description:

This superfamily includes Dehydroquinate synthase and Iron containing alcohol dehydrogenase which have a similar active site organisation [1].

The clan contains the following 3 members:

DHQ_synthase Fe-ADH Fe-ADH_2

Alignments

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  Seed
(95)
Full
(4669)
Representative proteomes NCBI
(3985)
Meta
(3068)
RP15
(401)
RP35
(765)
RP55
(1004)
RP75
(1160)
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  Seed
(95)
Full
(4669)
Representative proteomes NCBI
(3985)
Meta
(3068)
RP15
(401)
RP35
(765)
RP55
(1004)
RP75
(1160)
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Curation and family details

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Seed source: Pfam-B_1327 (release 4.2)
Previous IDs: none
Type: Domain
Author: Bashton M, Bateman A
Number in seed: 95
Number in full: 4669
Average length of the domain: 257.20 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 63.32 %

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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 24.2 24.2
Trusted cut-off 24.2 24.2
Noise cut-off 24.1 24.1
Model length: 261
Family (HMM) version: 15
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Interactions

There are 2 interactions for this family. More...

Fe-ADH DHQ_synthase

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 DHQ_synthase domain has been found. There are 45 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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