PDBsum entry: 1nvd

Lyase

PDB id: 1nvd

Contents

Protein chains

385 a.a. *

Ligands

CRB ×2

Metals

_ZN ×2

_CL

Waters ×694

* Residue conservation analysis

PDB id:

1nvd

Name:

Lyase

Title:

Crystal structure of 3-dehydroquinate synthase (dhqs) in complex with zn2+ and carbaphosphonate

Structure:

3-dehydroquinate synthase. Chain: a, b. Synonym: dhqs. Engineered: yes

Source:

Emericella nidulans. Organism_taxid: 162425. Gene: aroma. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.51Å R-factor: 0.196 R-free: 0.267

Authors:

C.E.Nichols,J.Ren,H.K.Lamb,A.R.Hawkins,D.K.Stammers

Key ref:

C.E.Nichols et al. (2003). Ligand-induced conformational changes and a mechanism for domain closure in Aspergillus nidulans dehydroquinate synthase. J Mol Biol, 327, 129-144. PubMed id: 12614613 DOI: 10.1016/S0022-2836(03)00086-X

Date:

03-Feb-03 Release date: 18-Mar-03

Protein chains

P07547  (ARO1_EMENI) -  Pentafunctional AROM polypeptide

Seq: 1583 a.a.

Struc: 385 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.1.1.1.25 - Shikimate dehydrogenase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: Shikimate + NADP⁺ = 3-dehydroshikimate + NADPH

Shikimate (Bound ligand (Het Group name = CRB) matches with 61.00% similarity) + NADP(+) = 3-dehydroshikimate + NADPH

• Enzyme class 3: E.C.2.5.1.19 - 3-phosphoshikimate 1-carboxyvinyltransferase.

Pathway:

• Reaction: Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O- (1-carboxyvinyl)-3-phosphoshikimate

Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O- (1-carboxyvinyl)-3-phosphoshikimate (Bound ligand (Het Group name = CRB) matches with 40.00% similarity)

• Enzyme class 4: E.C.2.7.1.71 - Shikimate kinase.

Pathway:

• Reaction: ATP + shikimate = ADP + shikimate 3-phosphate

ATP + shikimate (Bound ligand (Het Group name = CRB) matches with 61.00% similarity) = ADP + shikimate 3-phosphate

• Enzyme class 5: E.C.4.2.1.10 - 3-dehydroquinate dehydratase.

Pathway:

• Reaction: 3-dehydroquinate = 3-dehydroshikimate + H₂O

3-dehydroquinate (Bound ligand (Het Group name = CRB) matches with 66.00% similarity) = 3-dehydroshikimate + H(2)O

• Enzyme class 6: E.C.4.2.3.4 - 3-dehydroquinate synthase.

Pathway:

• Reaction: 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate

3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate (Bound ligand (Het Group name = CRB) matches with 66.00% similarity) + phosphate

• Cofactor: Cobalt; NAD(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: aromatic amino acid family biosynthetic process (1 term)
• Biochemical function: 3-dehydroquinate synthase activity (1 term)

reference

DOI no: 10.1016/S0022-2836(03)00086-X

J Mol Biol 327:129-144 (2003)

PubMed id: 12614613

Ligand-induced conformational changes and a mechanism for domain closure in Aspergillus nidulans dehydroquinate synthase.

C.E.Nichols, J.Ren, H.K.Lamb, A.R.Hawkins, D.K.Stammers.

ABSTRACT

In order to investigate systematically substrate and cofactor-induced conformational changes in the enzyme dehydroquinate synthase (DHQS), eight structures representing a series of differently liganded states have been determined in a total of six crystal forms. DHQS in the absence of the substrate analogue carbaphosphonate, either unliganded or in the presence of NAD or ADP, is in an open form where a relative rotation of 11-13 degrees between N and C-terminal domains occurs.Analysis of torsion angle difference plots between sets of structures reveals eight rearrangements that appear relevant to domain closure and a further six related to crystal packing. Overlapping 21 different copies of the individual N and C-terminal DHQS domains further reveals a series of pivot points about which these movements occur and illustrates the way in which widely separated secondary structure elements are mechanically inter-linked to form "composite elements", which propagate structural changes across large distances.This analysis has provided insight into the basis of DHQS ligand-initiated domain closure and gives rise to the proposal of an ordered sequence of events involving substrate binding, and local rearrangements within the active site that are propagated to the hinge regions, leading to closure of the active-site cleft.

Selected figure(s)

Figure 1.
Figure 1. (a) Representative 2F[o] -F[c] electron density map of DHQS open form, crystal VI, contoured at 1.1s. (b) Representative 2F[o]-F[c] electron density map of DHQS closed form, crystal I, contoured at 1.1s. (c) Combination diagram of transparent SURF molecular surface (2.0 Å probe) and cartoon format secondary structure definitions; DHQS open form, crystal II, chain B. (d) Combination diagram of transparent SURF molecular surface (2.0 Å probe) and cartoon format secondary structure definitions; DHQS closed form, crystal I, chain A. (e) Splined tube trace of C^a positions of DHQS with open-form (crystal II, chain B) co-ordinates traced in green and closed-form (crystal 1, chain A) in red. (f) Splined tube trace of C^a positions of DHQS for; clockwise from top left, NAD/CBP ternary, CBP binary, NAD binary complexes and apo enzyme showing ligands and elements PE1-PE3 and DE2-DE5. Colouring and space filling are according to temperature factor.

Figure 4.
Figure 4. Topological schematic showing reaction mechanism and linkage of catalytic residues to structural elements.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 129-144) copyright 2003.

Figures were selected by an automated process.