1wyu

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{{Seed}}
 
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[[Image:1wyu.png|left|200px]]
 
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==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form==
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The line below this paragraph, containing "STRUCTURE_1wyu", creates the "Structure Box" on the page.
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<StructureSection load='1wyu' size='340' side='right'caption='[[1wyu]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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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]] 2.1&#8491;</td></tr>
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<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>
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{{STRUCTURE_1wyu| PDB=1wyu | SCENE= }}
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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=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>
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</table>
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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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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyu_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1wyu ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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===Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form===
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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:15791207<ref>PMID:15791207</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_15791207}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1wyu" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 15791207 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15791207}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1WYU is a 8 chains 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=1WYU OCA].
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[[Category: Thermus thermophilus HB8]]
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[[Category: Kamiya N]]
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==Reference==
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[[Category: Kuramitsu S]]
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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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[[Category: Maoka N]]
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[[Category: Thermus thermophilus]]
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[[Category: Masui R]]
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[[Category: Kamiya, N.]]
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[[Category: Nakagawa N]]
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[[Category: Kuramitsu, S.]]
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[[Category: Nakai T]]
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[[Category: Maoka, N.]]
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[[Category: Masui, R.]]
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[[Category: Nakagawa, N.]]
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[[Category: Nakai, T.]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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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 Nov 16 11:14:36 2008''
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Current revision

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

PDB ID 1wyu

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