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| | ==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form== | | ==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form== |
| - | <StructureSection load='1wyu' size='340' side='right' caption='[[1wyu]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='1wyu' size='340' side='right'caption='[[1wyu]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wyu]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WYU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wyu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wyt|1wyt]], [[1wyv|1wyv]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyu OCA], [https://pdbe.org/1wyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyu RCSB], [https://www.ebi.ac.uk/pdbsum/1wyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyu ProSAT], [https://www.topsan.org/Proteins/RSGI/1wyu TOPSAN]</span></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>
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| - | <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=1wyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyu OCA], [http://pdbe.org/1wyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyu RCSB], [http://www.ebi.ac.uk/pdbsum/1wyu PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyu TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q5SKW8_THET8 Q5SKW8_THET8]] 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).[HAMAP-Rule:MF_00712][SAAS:SAAS023010_004_045580] [[http://www.uniprot.org/uniprot/GCSPB_THET8 GCSPB_THET8]] 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). | + | [https://www.uniprot.org/uniprot/Q5SKW8_THET8 Q5SKW8_THET8] 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).[HAMAP-Rule:MF_00712][SAAS:SAAS023010_004_045580] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyu_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyu_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thet8]] | + | [[Category: Large Structures]] |
| - | [[Category: Kamiya, N]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Kuramitsu, S]] | + | [[Category: Kamiya N]] |
| - | [[Category: Maoka, N]] | + | [[Category: Kuramitsu S]] |
| - | [[Category: Masui, R]] | + | [[Category: Maoka N]] |
| - | [[Category: Nakagawa, N]] | + | [[Category: Masui R]] |
| - | [[Category: Nakai, T]] | + | [[Category: Nakagawa N]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Nakai T]] |
| - | [[Category: Oxidoreductase]]
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| - | [[Category: Rsgi]]
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| Structural highlights
Function
Q5SKW8_THET8 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).[HAMAP-Rule:MF_00712][SAAS:SAAS023010_004_045580]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.,Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N. Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207
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