PDBsum entry 1e6c

Transferase

PDB id: 1e6c

Contents

Protein chains

170 a.a. *

Ligands

PO4 ×2

MPD ×5

MRD

Metals

_CL ×2

Waters ×214

* Residue conservation analysis

PDB id:

1e6c

Name:

Transferase

Title:

K15m mutant of shikimate kinase from erwinia chrysanthemi

Structure:

Shikimate kinase. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Erwinia chrysanthemi. Organism_taxid: 556. Gene: arol. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Monomer (from PDB file)

Resolution:

1.80Å R-factor: 0.188 R-free: 0.227

Authors:

J.Maclean,T.Krell,J.R.Coggins,A.J.Lapthorn

Key ref:

T.Krell et al. (2001). Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine. Protein Sci, 10, 1137-1149. PubMed id: 11369852

Date:

10-Aug-00 Release date: 20-Jun-01

Protein chains

P10880  (AROL_DICCH) -  Shikimate kinase 2 from Dickeya chrysanthemi

Seq: 173 a.a.

Struc: 170 a.a.*

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

Enzyme reactions

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

shikimate + ATP (Bound ligand (Het Group name = MPD) matches with 66.67% similarity) = 3-phosphoshikimate + ADP + H(+)

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

reference

Protein Sci 10:1137-1149 (2001)

PubMed id: 11369852

Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.

T.Krell, J.Maclean, D.J.Boam, A.Cooper, M.Resmini, K.Brocklehurst, S.M.Kelly, N.C.Price, A.J.Lapthorn, J.R.Coggins.

ABSTRACT

Shikimate kinase, despite low sequence identity, has been shown to be structurally a member of the nucleoside monophosphate (NMP) kinase family, which includes adenylate kinase. In this paper we have explored the roles of residues in the P-loop of shikimate kinase, which forms the binding site for nucleotides and is one of the most conserved structural features in proteins. In common with many members of the P-loop family, shikimate kinase contains a cysteine residue 2 amino acids upstream of the essential lysine residue; the side chains of these residues are shown to form an ion pair. The C13S mutant of shikimate kinase was found to be enzymatically active, whereas the K15M mutant was inactive. However, the latter mutant had both increased thermostability and affinity for ATP when compared to the wild-type enzyme. The structure of the K15M mutant protein has been determined at 1.8 A, and shows that the organization of the P-loop and flanking regions is heavily disturbed. This indicates that, besides its role in catalysis, the P-loop lysine also has an important structural role. The structure of the K15M mutant also reveals that the formation of an additional arginine/aspartate ion pair is the most likely reason for its increased thermostability. From studies of ligand binding it appears that, like adenylate kinase, shikimate kinase binds substrates randomly and in a synergistic fashion, indicating that the two enzymes have similar catalytic mechanisms.