2ivb: Difference between revisions

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 ==SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE==
-<StructureSection load='2ivb' size='340' side='right' caption='[[2ivb]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='2ivb' size='340' side='right'caption='[[2ivb]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ivb]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IVB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ivb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IVB FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dw9|1dw9]], [[1dwk|1dwk]], [[2ivg|2ivg]], [[2iu7|2iu7]], [[2iuo|2iuo]], [[2ivq|2ivq]], [[2iv1|2iv1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </span></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=2ivb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivb OCA], [https://pdbe.org/2ivb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ivb RCSB], [https://www.ebi.ac.uk/pdbsum/2ivb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ivb ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ivb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ivb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ivb RCSB], [http://www.ebi.ac.uk/pdbsum/2ivb PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivb_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/2ivb_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2ivb ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-BACKGROUND: Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. RESULTS: We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. CONCLUSIONS: The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.
-Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.,Walsh MA, Otwinowski Z, Perrakis A, Anderson PM, Joachimiak A Structure. 2000 May 15;8(5):505-14. PMID:10801492<ref>PMID:10801492</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Cyanase]]
 [[Category: Escherichia coli]]
-[[Category: Anderson, P M.]]
+[[Category: Large Structures]]
-[[Category: Guilloton, M.]]
+[[Category: Anderson PM]]
-[[Category: Joachimiak, A.]]
+[[Category: Guilloton M]]
-[[Category: Walsh, M A.]]
+[[Category: Joachimiak A]]
-[[Category: Cyanate degradation]]
+[[Category: Walsh MA]]
-[[Category: Lyase]]
-[[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]