PDBsum entry: 2hk7

Oxidoreductase

PDB id: 2hk7

Contents

Protein chains

269 a.a. *

Metals

_HG ×6

Waters ×96

* Residue conservation analysis

PDB id:

2hk7

Name:

Oxidoreductase

Title:

Crystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with mercury at 2.5 angstrom resolution

Structure:

Shikimate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: aroe. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.50Å R-factor: 0.229 R-free: 0.272

Authors:

J.H.Gan,P.Prabakaran,Y.J.Gu,M.Andrykovitch,Y.Li,H.H.Liu, H.Yan,X.Ji

Key ref:

J.Gan et al. (2007). Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism. Biochemistry, 46, 9513-9522. PubMed id: 17649975 DOI: 10.1021/bi602601e

Date:

03-Jul-06 Release date: 19-Jun-07

Protein chains

O67049  (AROE_AQUAE) -  Shikimate dehydrogenase

Seq: 269 a.a.

Struc: 269 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

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

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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: nucleotide binding (4 terms)

reference

DOI no: 10.1021/bi602601e

Biochemistry 46:9513-9522 (2007)

PubMed id: 17649975

Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.

J.Gan, Y.Wu, P.Prabakaran, Y.Gu, Y.Li, M.Andrykovitch, H.Liu, Y.Gong, H.Yan, X.Ji.

ABSTRACT

The shikimate biosynthetic pathway is essential to microorganisms, plants, and parasites but absent from mammals. Therefore, shikimate dehydrogenase (SD) and other enzymes in the pathway are attractive targets for developing nontoxic antimicrobial agents, herbicides, and antiparasite drugs. SD catalyzes the fourth reaction in the pathway, the nicotinamide adenine dinucleotide phosphate- (NADP-) dependent reduction of 3-dehydroshikimic acid to shikimic acid (SA), as well as its reverse, by the transfer of a hydride. Previous structural studies reveal that the enzyme exists in two major conformations, an open and a closed form. For the reaction to occur, it is believed that the catalytic complex assumes the closed conformation. Nonetheless, the only structure containing both SA and NADP+ exhibits an open conformation (PDB entry 2EV9). Here, we present two crystal structures of Aquifex aeolicus SD, including a ternary complex with both SA and NADP+, which assumes the closed conformation and therefore contains a catalytically competent active site. On the basis of preexisting and novel structural and biochemical data, a catalytic mechanism is proposed.