4X9M

Oxidized L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and proposed mechanism of l-alpha-glycerophosphate oxidase from Mycoplasma pneumoniae.

Elkhal, C.K.Kean, K.M.Parsonage, D.Maenpuen, S.Chaiyen, P.Claiborne, A.Karplus, P.A.

(2015) Febs J. 282: 3030-3042

  • DOI: 10.1111/febs.13233
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The formation of H2 O2 by the FAD-dependent L-α-glycerophosphate oxidase (GlpO) is important for the pathogenesis of Streptococcus pneumoniae and Mycoplasma pneumoniae. The structurally known GlpO from Streptococcus sp. (SspGlpO) is similar to the pn ...

    The formation of H2 O2 by the FAD-dependent L-α-glycerophosphate oxidase (GlpO) is important for the pathogenesis of Streptococcus pneumoniae and Mycoplasma pneumoniae. The structurally known GlpO from Streptococcus sp. (SspGlpO) is similar to the pneumococcal protein (SpGlpO) and provides a guide for drug design against that target. However, M. pneumoniae GlpO (MpGlpO), having < 20% sequence identity with structurally known GlpOs, appears to represent a second type of GlpO that we designate as type II GlpOs. In the present study, the recombinant His-tagged MpGlpO structure is described at an approximate resolution of 2.5 Å, solved by molecular replacement using, as a search model, the Bordetella pertussis protein 3253 (Bp3253), comprising a protein of unknown function solved by structural genomics efforts. Recombinant MpGlpO is an active oxidase with a turnover number of approximately 580 min(-1), whereas Bp3253 showed no GlpO activity. No substantial differences exist between the oxidized and dithionite-reduced MpGlpO structures. Although, no liganded structures were determined, a comparison with the tartrate-bound Bp3253 structure and consideration of residue conservation patterns guided the construction of a model for L-α-glycerophosphate (Glp) recognition and turnover by MpGlpO. The predicted binding mode also appears relevant for the type I GlpOs (such as SspGlpO) despite differences in substrate recognition residues, and it implicates a histidine conserved in type I and II Glp oxidases and dehydrogenases as the catalytic acid/base. The present study provides a solid foundation for guiding further studies of the mitochondrial Glp dehydrogenases, as well as for continued studies of M. pneumoniae and S. pneumoniae glycerol metabolism and the development of novel therapeutics targeting MpGlpO and SpGlpO.


    Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand.,Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-alpha-glycerophosphate oxidase
A
418Mycoplasma pneumoniae (strain ATCC 29342 / M129)Mutation(s): 0 
Find proteins for P75063 (Mycoplasma pneumoniae (strain ATCC 29342 / M129))
Go to UniProtKB:  P75063
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
G3P
Query on G3P

Download SDF File 
Download CCD File 
A
SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.148 
  • Space Group: P 2 3
Unit Cell:
Length (Å)Angle (°)
a = 111.590α = 90.00
b = 111.590β = 90.00
c = 111.590γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2015-09-02
    Type: Database references