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| - | [[Image:2agk.gif|left|200px]] | |
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| - | {{Structure
| + | ==Structure of S. cerevisiae His6 protein== |
| - | |PDB= 2agk |SIZE=350|CAPTION= <scene name='initialview01'>2agk</scene>, resolution 1.300Å
| + | <StructureSection load='2agk' size='340' side='right'caption='[[2agk]], [[Resolution|resolution]] 1.30Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> | + | <table><tr><td colspan='2'>[[2agk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AGK FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3Å</td></tr> |
| - | |GENE= YIL020c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2agk OCA], [https://pdbe.org/2agk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2agk RCSB], [https://www.ebi.ac.uk/pdbsum/2agk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2agk ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2agk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2agk OCA], [http://www.ebi.ac.uk/pdbsum/2agk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2agk RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/HIS4_YEAST HIS4_YEAST] Catalyzes the isomerization of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR. |
| - | | + | == Evolutionary Conservation == |
| - | '''Structure of S. cerevisiae His6 protein'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ag/2agk_consurf.spt"</scriptWhenChecked> |
| - | The Saccharomyces cerevisiae His6 gene codes for the enzyme phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase, catalyzing the fourth step in histidine biosynthesis. To get an insight into the structure and function of this enzyme, we determined its X-ray structure at a resolution of 1.30 A using the anomalous diffraction signal of the protein's sulphur atoms at 1.77 A wavelength. His6 folds in an (alpha/beta)8 barrel similar to HisA, which performs the same function in bacteria and archaea. We found a citrate molecule from the buffer bound in a pocket near the expected position of the active site and used it to model the open form of the substrate (phosphoribulosyl moiety), which is a reaction intermediate. This model enables us to identify catalytic residues and to propose a reaction mechanism where two aspartates act as acid/base catalysts: Asp134 as a proton donor for ring opening, and Asp9 as a proton acceptor and donor during enolization of the aminoaldose. Asp9 is conserved in yeast His6 and bacterial or archaeal HisA sequences, and Asp134 has equivalents in both HisA and TrpF, but they occur at a different position in the protein sequence.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 2AGK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AGK OCA].
| + | </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=2agk ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | __TOC__ |
| - | Crystal structure of the yeast His6 enzyme suggests a reaction mechanism., Quevillon-Cheruel S, Leulliot N, Graille M, Blondeau K, Janin J, van Tilbeurgh H, Protein Sci. 2006 Jun;15(6):1516-21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16731983 16731983]
| + | </StructureSection> |
| - | [[Category: 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase]] | + | [[Category: Large Structures]] |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Single protein]]
| + | [[Category: Tilbeurgh HV]] |
| - | [[Category: Tilbeurgh, H V.]] | + | |
| - | [[Category: YSG, Paris-Sud Yeast Structural Genomics.]]
| + | |
| - | [[Category: paris-sud yeast structural genomic]]
| + | |
| - | [[Category: s. cerevisiae structural genomics project]]
| + | |
| - | [[Category: structural genomic]]
| + | |
| - | [[Category: tim alpha/beta barrel]]
| + | |
| - | [[Category: ysg]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:52:24 2008''
| + | |
