PDBsum entry 4zky

Oxidoreductase

PDB id: 4zky

Contents

Protein chains

139 a.a.

Metals

_CL

_NA

IOD

Waters ×164

PDB id:

4zky

Name:

Oxidoreductase

Title:

Structure of f420 binding protein, msmeg_6526, from mycobacterium smegmatis

Structure:

Pyridoxamine 5-phosphate oxidase. Chain: a, b. Engineered: yes

Source:

Mycobacterium smegmatis. Organism_taxid: 1772. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.65Å R-factor: 0.224 R-free: 0.259

Authors:

B.M.Lee,P.D.Carr,F.H.Ahmed,C.J.Jackson

Key ref:

F.H.Ahmed et al. (2015). Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. J Mol Biol, 427, 3554-3571. PubMed id: 26434506 DOI: 10.1016/j.jmb.2015.09.021

Date:

01-May-15 Release date: 28-Oct-15

Protein chains

A0R6F1  (A0R6F1_MYCS2) -  Pyridoxamine 5'-phosphate oxidase family protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)

Seq: 142 a.a.

Struc: 139 a.a.

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: 10.1016/j.jmb.2015.09.021

J Mol Biol 427:3554-3571 (2015)

PubMed id: 26434506

Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.

F.H.Ahmed, P.D.Carr, B.M.Lee, L.Afriat-Jurnou, A.E.Mohamed, N.S.Hong, J.Flanagan, M.C.Taylor, C.Greening, C.J.Jackson.

ABSTRACT

The deazaflavin cofactor F420 enhances the persistence of mycobacteria during hypoxia, oxidative stress, and antibiotic treatment. However, the identities and functions of the mycobacterial enzymes that utilize F420 under these conditions have yet to be resolved. In this work, we used sequence similarity networks to analyze the distribution of the largest F420-dependent protein family in mycobacteria. We show that these enzymes are part of a larger split β-barrel enzyme superfamily (flavin/deazaflavin oxidoreductases, FDORs) that include previously characterized pyridoxamine/pyridoxine-5'-phosphate oxidases and heme oxygenases. We show that these proteins variously utilize F420, flavin mononucleotide, flavin adenine dinucleotide, and heme cofactors. Functional annotation using phylogenetic, structural, and spectroscopic methods revealed their involvement in heme degradation, biliverdin reduction, fatty acid modification, and quinone reduction. Four novel crystal structures show that plasticity in substrate binding pockets and modifications to cofactor binding motifs enabled FDORs to carry out a variety of functions. This systematic classification and analysis provides a framework for further functional analysis of the roles of FDORs in mycobacterial pathogenesis and persistence.