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

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1111/febs.13233
  • Primary Citation of Related Structures:  
    4X9M, 4X9N

  • 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 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 and Biophysics, Oregon State University, Corvallis, OR, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-alpha-glycerophosphate oxidase418Mycoplasmoides pneumoniae M129Mutation(s): 0 
Gene Names: MPN_051D09_orf384MP103
Find proteins for P75063 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75063 
Go to UniProtKB:  P75063
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75063
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.59α = 90
b = 111.59β = 90
c = 111.59γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2015-09-02
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description