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52  structures 1982  species 2  interactions 2260  sequences 37  architectures

Family: DHquinase_I (PF01487)

Summary: Type I 3-dehydroquinase

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

3-dehydroquinate dehydratase Edit Wikipedia article

3-dehydroquinate dehydratase
DHQDrxnCMDR.png
The third step of the shikimate pathway is catalyzed by DHQD
Identifiers
EC number 4.2.1.10
CAS number 9012-66-2
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
Type I 3-dehydroquinase
PDB 1qfe EBI.jpg
The structure of type i 3-dehydroquinate dehydratase from salmonella typhi
Identifiers
Symbol DHquinase_I
Pfam PF01487
Pfam clan CL0036
InterPro IPR001381
PROSITE PDOC00789
SCOP 2dhq
SUPERFAMILY 2dhq
Dehydroquinase class II
Identifiers
Symbol DHquinase_II
Pfam PF01220
PROSITE PDOC00789
SCOP 2dhq
SUPERFAMILY 2dhq

In enzymology, a 3-dehydroquinate dehydratase (EC 4.2.1.10) is an enzyme that catalyzes the chemical reaction

3-dehydroquinate \rightleftharpoons 3-dehydroshikimate + H2O

Hence, this enzyme has one substrate, 3-dehydroquinate, and two products, 3-dehydroshikimate and H2O.

This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis.

Discovery

The shikimate pathway was determined to be a major biosynthetic route for the production of aromatic amino acids through the research of Bernhard Davis and David Sprinson.[1]

Role in the shikimate pathway

3-Dehydroquinate Dehydratase is an enzyme that catalyzes the third step of the shikimate pathway. The shikimate pathway is a biosynthetic pathway that allows plants, fungi, and bacteria to produce aromatic amino acids.[2] Mammals do not have this pathway, meaning that they must obtain these essential amino acids through their diet. Aromatic Amino acids include Phenylalanine, Tyrosine, and Tryptophan.[1]

This enzyme dehydrates 3-Dehydroquinate, converting it to 3-Dehydroshikimate, as indicated in the diagram on the right. This is the third step in the Shikimate pathway. It belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic name of this enzyme class is 3-dehydroquinate hydro-lyase (3-dehydroshikimate-forming). This enzyme is one of the few examples of convergent evolution. The two separate versions of this enzyme have different amino acid sequences.[2]

3-Dehydroquinate dehydratase is also commonly referred to as Dehydroquinate dehydratase and DHQD. Other names include 3-dehydroquinate hydrolase, DHQase, 3-dehydroquinase, 5-dehydroquinase, dehydroquinase, 5-dehydroquinate dehydratase, 5-dehydroquinate hydro-lyase, and 3-dehydroquinate hydro-lyase.[2]

Cartoon view of 2EGZ DHQD. The alpha helices are displayed in red, and the beta sheets are displayed in yellow. (Created using MacPyMol)

Evolutionary origins

Purposes of the products

The aromatic amino acids produced by the shikimate acid pathway are used by higher plants as protein building blocks and as precursors for several secondary metabolites. Examples of such secondary metabolites are plant pigments and compounds to defend against herbivores, insects, and UV light. The specific aromatic secondary metabolites produced, as well as when and in what quantities they are produced in, varies across different types of plants. Mammals consume essential amino acids in their diets, converting them to precursors for important substances such as neurotransmitters.

Convergent evolution

As mentioned previously, two classes of 3-Dehydroquinate Dehydratase exist, known as types I and II. These two versions have different amino acid sequences and different secondary structures. Type I is present in fungi, plants, and some bacteria, for the biosynthesis of chorismate. It catalyzes the cis-dehydration of 3-Dehydroquinate via a covalent imine intermediate. Type I is heat liable and has Km values in the low micromolar range. Type II is present in the quinate pathway of fungi and the shikimate pathway of most bacteria. It catalyzes a trans-dehydration using an enolate intermediate. It is heat stable and has Km values one or two orders of magnitude higher than the Type I Km values.[1]

The best studied type I enzyme is from Escherichia coli (gene aroD) and related bacteria. It is a homodimeric protein. In fungi, dehydroquinase is part of a multifunctional enzyme which catalyses five consecutive steps in the shikimate pathway. A histidine is involved in the catalytic mechanism.[3]

Other purposes

3-Dehydroquinate Dehydratase is also an enzyme present in the process of the degradation of quinate. Both 3-Dehydroquinate and 3-Dehydroshikimate are intermediates in the reaction mechanism. The following image shows this process in Quinate Degradation.[1]

One of the reactions that leads to the degradation of Quinate through the enzyme DHQD

Structure

Image of 2EGZ DHQD. Both monomers of the enzyme are visible. The R groups of the amino acids can be seen as the sticks extending from the exterior of the enzyme. This image is color-coded to display Oxygen (red), Nitrogen (Blue), and the backbone of the protein (yellow fading to green). (Created using MacPyMol)

Applications

The Shikimate pathway has become a focus of research into the development of herbicides and antimicrobial agents because it is an essential pathway in many plants, bacteria, and parasites but does not exist in mammals.[1]

Inhibitors of the shikimate pathway in mycobacterium have the potential of treating tuberculosis.[4][5]

Most of the 3-dehydroquinate-dehydratase in bacteria and higher plants is type I DHQD.[1]

References

  1. ^ a b c d e f Herrmann KM (July 1995). "The Shikimate Pathway: Early Steps in the Biosynthesis of Aromatic Compounds". Plant Cell 7 (7): 907–919. doi:10.1105/tpc.7.7.907. PMC 160886. PMID 12242393. 
  2. ^ a b c Herrmann KM (January 1995). "The shikimate pathway as an entry to aromatic secondary metabolism". Plant Physiol. 107 (1): 7–12. doi:10.1104/pp.107.1.7. PMC 161158. PMID 7870841. 
  3. ^ Deka RK, Kleanthous C, Coggins JR (November 1992). "Identification of the essential histidine residue at the active site of Escherichia coli dehydroquinase". J. Biol. Chem. 267 (31): 22237–42. PMID 1429576. 
  4. ^ Dias MV, Snee WC, Bromfield KM, Payne RJ, Palaninathan SK, Ciulli A, Howard NI, Abell C, Sacchettini JC, Blundell TL (June 2011). "Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis". Biochem. J. 436 (3): 729–39. doi:10.1042/BJ20110002. PMID 21410435. 
  5. ^ Reichau S, Jiao W, Walker SR, Hutton RD, Baker EN, Parker EJ (May 2011). "Potent inhibitors of a shikimate pathway enzyme from Mycobacterium tuberculosis: combining mechanism- and modeling-based design". J. Biol. Chem. 286 (18): 16197–207. doi:10.1074/jbc.M110.211649. PMC 3093739. PMID 21454647. 

Further reading

  • Mitsuhashi S, Davis BD (1954). "Aromatic biosynthesis. XII. Conversion of 5-dehydroquinic acid to 5-dehydroshikimic acid dy 5-dehydroquinase". Biochim. Biophys. Acta. 15 (1): 54–61. doi:10.1016/0006-3002(54)90093-1. PMID 13198937. 
  • Mitsuhashi S, Davis BD (1954). "Aromatic biosynthesis. XIII. Conversion of quinic acid to 5-dehydroquinic acid by quinic dehydrogenase". Biochim. Biophys. Acta. 15 (2): 268–80. doi:10.1016/0006-3002(54)90069-4. PMID 13208693. 

This article incorporates text from the public domain Pfam and InterPro IPR001381

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

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Type I 3-dehydroquinase Provide feedback

Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see PF01220.

Literature references

  1. Gourley DG, Shrive AK, Polikarpov I, Krell T, Coggins JR, Hawkins AR, Isaacs NW, Sawyer L; , Nat Struct Biol 1999;6:521-525.: The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction. PUBMED:10360352 EPMC:10360352

  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.

InterPro entry IPR001381

3-dehydroquinate dehydratase (EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II.

The best studied type I enzyme is from Escherichia coli (gene aroD) and related bacteria where it is a homodimeric protein. In fungi, dehydroquinase is part of a multifunctional enzyme which catalyzes five consecutive steps in the shikimate pathway. A histidine [PUBMED:1429576] is involved in the catalytic mechanism.

Gene Ontology

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Seed source: Pfam-B_2492 (release 4.0)
Previous IDs: none
Type: Domain
Author: Bashton M, Bateman A
Number in seed: 150
Number in full: 2260
Average length of the domain: 219.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 56.47 %

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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 20.7 20.7
Trusted cut-off 20.9 21.2
Noise cut-off 20.6 19.7
Model length: 224
Family (HMM) version: 10
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Interactions

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

DHquinase_I Shikimate_dh_N

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 DHquinase_I domain has been found. There are 52 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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