PDBsum entry 2ddm

Transferase

PDB id: 2ddm

Contents

Protein chains

264 a.a. *

Ligands

TRS ×2

Waters ×407

* Residue conservation analysis

PDB id:

2ddm

Name:

Transferase

Title:

Crystal structure of pyridoxal kinase from the escherichia coli pdxk gene at 2.1 a resolution

Structure:

Pyridoxine kinase. Chain: a, b. Synonym: pyridoxal kinase, vitamin b6 kinase, pyridoxamine kinase, pn/pl/pm kinase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: hms 174(de3). Gene: pdxk. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.194 R-free: 0.218

Authors:

M.K.Safo,F.N.Musayev,M.L.Di Salvo,S.Hunt,J.B.Claude,V.Schirch

Key ref:

M.K.Safo et al. (2006). Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases. J Bacteriol, 188, 4542-4552. PubMed id: 16740960

Date:

02-Feb-06 Release date: 15-Aug-06

Protein chains

P40191  (PDXK_ECOLI) -  Pyridoxine/pyridoxal/pyridoxamine kinase from Escherichia coli (strain K12)

Seq: 283 a.a.

Struc: 264 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.35 - pyridoxal kinase.
• Reaction: pyridoxal + ATP = pyridoxal 5'-phosphate + ADP + H⁺

pyridoxal + ATP (Bound ligand (Het Group name = TRS) matches with 42.86% similarity) = pyridoxal 5'-phosphate + ADP + H(+)

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

reference

J Bacteriol 188:4542-4552 (2006)

PubMed id: 16740960

Crystal structure of pyridoxal kinase from the Escherichia coli pdxK gene: implications for the classification of pyridoxal kinases.

M.K.Safo, F.N.Musayev, M.L.di Salvo, S.Hunt, J.B.Claude, V.Schirch.

ABSTRACT

The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-A resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4' substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4' of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.