1wyv

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[[Image:1wyv.gif|left|200px]]
 
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{{Structure
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==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==
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|PDB= 1wyv |SIZE=350|CAPTION= <scene name='initialview01'>1wyv</scene>, resolution 2.40&Aring;
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<StructureSection load='1wyv' size='340' side='right'caption='[[1wyv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene>
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<table><tr><td colspan='2'>[[1wyv]] 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=1WYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYV FirstGlance]. <br>
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|ACTIVITY= [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]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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|GENE= GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [https://pdbe.org/1wyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [https://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [https://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
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</table>
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'''Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form'''
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== Function ==
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[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]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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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.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyv_consurf.spt"</scriptWhenChecked>
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1WYV is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYV OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15791207 15791207]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wyv ConSurf].
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[[Category: Glycine dehydrogenase (decarboxylating)]]
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<div style="clear:both"></div>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Thermus thermophilus]]
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</StructureSection>
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[[Category: Kamiya, N.]]
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[[Category: Large Structures]]
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[[Category: Kuramitsu, S.]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Maoka, N.]]
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[[Category: Kamiya N]]
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[[Category: Masui, R.]]
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[[Category: Kuramitsu S]]
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[[Category: Nakagawa, N.]]
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[[Category: Maoka N]]
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[[Category: Nakai, T.]]
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[[Category: Masui R]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Nakagawa N]]
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[[Category: PLP]]
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[[Category: Nakai T]]
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[[Category: alpha(2)beta(2) tetramer]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 14:09:59 2008''
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Current revision

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form

PDB ID 1wyv

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