Summary: Type I 3-dehydroquinase
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3-dehydroquinate dehydratase Edit Wikipedia article
The third step of the shikimate pathway is catalyzed by DHQD
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
|Type I 3-dehydroquinase|
The structure of type i 3-dehydroquinate dehydratase from salmonella typhi
|Dehydroquinase class II|
- 3-dehydroquinate 3-dehydroshikimate + 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.
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. 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.
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.
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.
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.
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.
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-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.
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.
Most of the 3-dehydroquinate-dehydratase in bacteria and higher plants is type I DHQD.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
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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.
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
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 catalyses five consecutive steps in the shikimate pathway. A histidine [PUBMED:1429576] is involved in the catalytic mechanism.
This entry represents the 3-dehydroquinate dehydratase, type I, either as a monofunctional protein or as a domain of a larger, multifunctional protein.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||3-dehydroquinate dehydratase activity (GO:0003855)|
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This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 57 members:Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI Pterin_bind QRPTase_C Radical_SAM RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiC_Rad_SAM ThiG TIM TMP-TENI Transaldolase Trp_syntA UvdE UxuA
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|Seed source:||Pfam-B_2492 (release 4.0)|
|Author:||Bashton M, Bateman A|
|Number in seed:||248|
|Number in full:||1013|
|Average length of the domain:||217.60 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||32.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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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 82 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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