4LGL

Crystal Structure of Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803, apo form

Summary for 4LGL

• Entry DOI: 10.2210/pdb4lgl/pdb
• Related: 4LHC 4LHD
• Descriptor: Glycine dehydrogenase [decarboxylating], 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: alpha(2) homodimeric, dehydrogenase (decarboxylating), s, s-(2-hydroxyethyl)thiocysteine, oxidoreductase
• Biological source: Synechocystis sp.
• Total number of polymer chains: 2
• Total formula weight: 215461.77

Authors

Hasse, D.,Andersson, E.,Carlsson, G.,Masloboy, A.,Hagemann, M.,Bauwe, H.,Andersson, I. (deposition date: 2013-06-28, release date: 2013-10-16, Last modification date: 2023-09-20)

Primary citation

Hasse, D.,Andersson, E.,Carlsson, G.,Masloboy, A.,Hagemann, M.,Bauwe, H.,Andersson, I.
Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox Regulation.
J.Biol.Chem., 288:35333-35345, 2013

PubMed Abstract: Glycine decarboxylase, or P-protein, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. P-protein from the cyanobacterium Synechocystis sp. PCC 6803 is an α2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apoenzyme shows the C terminus locked in a closed conformation by a disulfide bond between Cys(972) in the C terminus and Cys(353) located in the active site. The presence of the disulfide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys(972) and Cys(353) by Ser using site-directed mutagenesis have distinctly lower specific activities, supporting the crucial role of these highly conserved redox-sensitive amino acid residues for P-protein activity. Reduction of the 353-972 disulfide releases the C terminus and allows access to the active site. PLP and the substrate glycine bind in the active site of this reduced enzyme and appear to cause further conformational changes involving a flexible surface loop. The observation of the disulfide bond that acts to stabilize the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier.

PubMed: 24121504
DOI: 10.1074/jbc.M113.509976

Experimental method

X-RAY DIFFRACTION (2.0004 Å)