PDBsum entry: 2iyz

Transferase

PDB id: 2iyz

Contents

Protein chain

168 a.a. *

Ligands

S3P

ADP

Waters ×173

* Residue conservation analysis

PDB id:

2iyz

Name:

Transferase

Title:

Shikimate kinase from mycobacterium tuberculosis in complex with shikimate-3-phosphate and adp

Structure:

Shikimate kinase. Chain: a. Synonym: sk. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Atcc: 25618. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.30Å R-factor: 0.193 R-free: 0.242

Authors:

M.D.Hartmann,G.P.Bourenkov,A.Oberschall,N.Strizhov, H.D.Bartunik

Key ref:

M.D.Hartmann et al. (2006). Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol, 364, 411-423. PubMed id: 17020768 DOI: 10.1016/j.jmb.2006.09.001

Date:

22-Jul-06 Release date: 11-Oct-06

Protein chain

P0A4Z2  (AROK_MYCTU) -  Shikimate kinase

Seq: 176 a.a.

Struc: 168 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.71 - Shikimate kinase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: ATP + shikimate = ADP + shikimate 3-phosphate

ATP + shikimate = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + shikimate 3-phosphate (Bound ligand (Het Group name = S3P) corresponds exactly)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: growth (3 terms)
• Biochemical function: nucleotide binding (6 terms)

reference

DOI no: 10.1016/j.jmb.2006.09.001

J Mol Biol 364:411-423 (2006)

PubMed id: 17020768

Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis.

M.D.Hartmann, G.P.Bourenkov, A.Oberschall, N.Strizhov, H.D.Bartunik.

ABSTRACT

The structural mechanism of the catalytic functioning of shikimate kinase from Mycobacterium tuberculosis was investigated on the basis of a series of high-resolution crystal structures corresponding to individual steps in the enzymatic reaction. The catalytic turnover of shikimate and ATP into the products shikimate-3-phosphate and ADP, followed by release of ADP, was studied in the crystalline environment. Based on a comparison of the structural states before initiation of the reaction and immediately after the catalytic step, we derived a structural model of the transition state that suggests that phosphoryl transfer proceeds with inversion by an in-line associative mechanism. The random sequential binding of shikimate and nucleotides is associated with domain movements. We identified a synergic mechanism by which binding of the first substrate may enhance the affinity for the second substrate.

Selected figure(s)

Figure 1.
Figure 1. Atom nomenclature for SKM and S3P. The SKM nomenclature is similar to that used previously.^13 The schemes were produced with ChemDraw.

Figure 2.
Figure 2. Ribbon representation of apo-MtSK with open LID conformation. All molecular depictions were produced with MolScript,^37 BOBSCRIPT^38 and Raster3D.^39

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 411-423) copyright 2006.

Figures were selected by an automated process.