4lhc: Difference between revisions
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The | ==Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine== | ||
<StructureSection load='4lhc' size='340' side='right' caption='[[4lhc]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4lhc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LHC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LHC FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lgl|4lgl]], [[4lhd|4lhd]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gcvP, slr0293 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lhc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lhc OCA], [http://pdbe.org/4lhc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lhc RCSB], [http://www.ebi.ac.uk/pdbsum/4lhc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lhc ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/GCSP_SYNY3 GCSP_SYNY3]] The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 alpha2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apo enzyme shows the C-terminus locked in a closed conformation by a disulphide bond between Cys972 in the C-terminus and Cys353 located in the active site. Presence of the disulphide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys972 and Cys353 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 disulphide 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 disulphide bond that acts to stabilise the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier. | |||
Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox-Regulation.,Hasse D, Andersson E, Carlsson G, Masloboy A, Hagemann M, Bauwe H, Andersson I J Biol Chem. 2013 Oct 11. PMID:24121504<ref>PMID:24121504</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4lhc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Syny3]] | |||
[[Category: Andersson, E]] | |||
[[Category: Andersson, I]] | |||
[[Category: Bauwe, H]] | |||
[[Category: Carlsson, G]] | |||
[[Category: Hagemann, M]] | |||
[[Category: Hasse, D]] | |||
[[Category: Masloboy, A]] | |||
[[Category: Cofactor pyridoxal 5'-phosphate]] | |||
[[Category: Oxidoreductase]] | |||
Latest revision as of 04:11, 5 August 2016
Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycineCrystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine
Structural highlights
Function[GCSP_SYNY3] The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity). Publication Abstract from PubMedGlycine 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 alpha2 homodimer with high homology to eukaryotic P-proteins. The crystal structure of the apo enzyme shows the C-terminus locked in a closed conformation by a disulphide bond between Cys972 in the C-terminus and Cys353 located in the active site. Presence of the disulphide bridge isolates the active site from solvent and hinders the binding of PLP and glycine in the active site. Variants produced by substitution of Cys972 and Cys353 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 disulphide 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 disulphide bond that acts to stabilise the closed form suggests a molecular mechanism for the redox-dependent activation of glycine decarboxylase observed earlier. Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox-Regulation.,Hasse D, Andersson E, Carlsson G, Masloboy A, Hagemann M, Bauwe H, Andersson I J Biol Chem. 2013 Oct 11. PMID:24121504[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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