4X9N

Dithionite reduced L-alpha-Glycerophosphate Oxidase from Mycoplasma pneumoniae with FAD bound

Summary for 4X9N

• Entry DOI: 10.2210/pdb4x9n/pdb
• Related: 4X9M
• Descriptor: L-alpha-glycerophosphate oxidase, FLAVIN-ADENINE DINUCLEOTIDE, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: flavoenzyme, oxidase, glycerol-3-phosphate oxidase, glycerol-3-phosphate dehydrogenase, oxidoreductase
• Biological source: Mycoplasma pneumoniae (strain ATCC 29342 / M129)
• Total number of polymer chains: 1
• Total formula weight: 47176.55

Authors

Elkhal, C.K.,Kean, K.M.,Parsonage, D.,Claiborne, A.,Karplus, P.A. (deposition date: 2014-12-11, release date: 2015-03-04, Last modification date: 2024-10-23)

Primary citation

Elkhal, C.K.,Kean, K.M.,Parsonage, D.,Maenpuen, S.,Chaiyen, P.,Claiborne, A.,Karplus, P.A.
Structure and proposed mechanism of l-alpha-glycerophosphate oxidase from Mycoplasma pneumoniae.
Febs J., 282:3030-3042, 2015

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.

PubMed: 25688572
DOI: 10.1111/febs.13233

Experimental method

X-RAY DIFFRACTION (2.499 Å)