PDBsum entry 2a2j

Oxidoreductase

PDB id: 2a2j

Contents

Protein chains

203 a.a. *

Waters ×75

* Residue conservation analysis

PDB id:

2a2j

Name:

Oxidoreductase

Title:

Crystal structure of a putative pyridoxine 5'-phosphate oxidase (rv2607) from mycobacterium tuberculosis

Structure:

Pyridoxamine 5'-phosphate oxidase. Chain: a, b. Synonym: pnp/pmp oxidase, pnpox. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.213 R-free: 0.260

Authors:

J.-D.Pedelacq,B.-S.Rho,C.-Y.Kim,G.S.Waldo,T.P.Lekin,B.W.Segelke, B.Rupp,L.-W.Hung,S.-I.Kim,T.C.Terwilliger,Mycobacterium Tuberculosis Structural Proteomics Project (Xmtb)

Key ref:

J.D.Pédelacq et al. (2006). Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis. Proteins, 62, 563-569. PubMed id: 16374842 DOI: 10.1002/prot.20824

Date:

22-Jun-05 Release date: 23-Aug-05

Protein chains

P9WIJ1  (PDXH_MYCTU) -  Pyridoxine 5'-phosphate oxidase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 224 a.a.

Struc: 203 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.4.3.5 - pyridoxal 5'-phosphate synthase.
• Reaction:
  1. pyridoxamine 5'-phosphate + O2 + H2O = pyridoxal 5'-phosphate + H2O2 + NH4⁺
  2. pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2
• Cofactor: FMN

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

reference

DOI no: 10.1002/prot.20824

Proteins 62:563-569 (2006)

PubMed id: 16374842

Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis.

J.D.Pédelacq, B.S.Rho, C.Y.Kim, G.S.Waldo, T.P.Lekin, B.W.Segelke, B.Rupp, L.W.Hung, S.I.Kim, T.C.Terwilliger.

ABSTRACT

The three-dimensional structure of Rv2607, a putative pyridoxine 5'-phosphate oxidase (PNPOx) from Mycobacterium tuberculosis, has been determined by X-ray crystallography to 2.5 A resolution. Rv2607 has a core domain similar to known PNPOx structures with a flavin mononucleotide (FMN) cofactor. Electron density for two FMN at the dimer interface is weak despite the bright yellow color of the protein solution and crystal. The shape and size of the putative binding pocket is markedly different from that of members of the PNPOx family, which may indicate some significant changes in the FMN binding mode of this protein relative to members of the family.

Selected figure(s)

Figure 1.
Figure 1. Representation of the three-dimensional structure of (A) Rv2607 and (B) the E. coli oxidase (PDB code: 1G79). (C) Structure-based sequence alignment. strands are shown as arrows and helices as coils. Sequence homologies are highlighted in red; sequence identities are shown as white letters on a red background. Residues important for FMN binding, PLP binding, and both, are indicated using yellow, blue, and green triangles, respectively.

Figure 4.
Figure 4. Stereo view of the active site. (A) Stereo diagrams of 2Fo-Fc map at 1 level (blue) and Fo-Fc map at 3 level (red). Only the residues within 5 Å of the FMN in Rv2607 are shown in ball-and-stick representation. (B) Superimposition of Rv2607 (yellow) and the E. coli oxidase (pink) with FMN (PDB code: 1G79). (C) Superimposition of Rv2607 (yellow) and the E. coli oxidase (pink) in complex with PLP (PDB code: 1G79).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 563-569) copyright 2006.

Figures were selected by an automated process.