PDBsum entry 2dft

Transferase

PDB id: 2dft

Contents

Protein chains

156 a.a. *

165 a.a. *

Ligands

ADP ×4

Metals

_MG ×4

_CL ×3

Waters ×260

* Residue conservation analysis

PDB id:

2dft

Name:

Transferase

Title:

Structure of shikimate kinase from mycobacterium tuberculosis complexed with adp and mg at 2.8 angstrons of resolution

Structure:

Shikimate kinase. Chain: a, b, c, d. Synonym: sk. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: arok. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.80Å R-factor: 0.183 R-free: 0.282

Authors:

M.V.Dias,L.M.Faim,I.B.Vasconcelos,J.S.De Oliveira,L.A.Basso, D.S.Santos,W.F.De Azevedo

Key ref:

M.V.Dias et al. (2007). Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1-6. PubMed id: 17183161

Date:

03-Mar-06 Release date: 16-Jan-07

Protein chains

P9WPY3  (AROK_MYCTU) -  Shikimate kinase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 176 a.a.

Struc: 156 a.a.

Protein chains

P9WPY3  (AROK_MYCTU) -  Shikimate kinase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 176 a.a.

Struc: 165 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.2.7.1.71 - shikimate kinase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: shikimate + ATP = 3-phosphoshikimate + ADP + H⁺

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

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

reference

Acta Crystallogr Sect F Struct Biol Cryst Commun 63:1-6 (2007)

PubMed id: 17183161

Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis.

M.V.Dias, L.M.Faím, I.B.Vasconcelos, J.S.de Oliveira, L.A.Basso, D.S.Santos, W.F.de Azevedo.

ABSTRACT

Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts shikimate to shikimate-3-phosphate. In this work, the conformational changes that occur on binding of shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.