3ivz
From Proteopedia
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| - | {{STRUCTURE_3ivz| PDB=3ivz | SCENE= }} | ||
| - | ===Crystal structure of hyperthermophilic nitrilase=== | ||
| - | {{ABSTRACT_PUBMED_21095228}} | ||
| - | == | + | ==Crystal structure of hyperthermophilic nitrilase== |
| - | [[3ivz]] is a 2 chain structure with sequence from [ | + | <StructureSection load='3ivz' size='340' side='right'caption='[[3ivz]], [[Resolution|resolution]] 1.57Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3ivz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IVZ FirstGlance]. <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]] 1.57Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=3ivz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ivz OCA], [https://pdbe.org/3ivz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ivz RCSB], [https://www.ebi.ac.uk/pdbsum/3ivz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ivz ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/NITR_PYRAB NITR_PYRAB] Nitrilase that hydrolyzes preferentially aliphatic nitriles like malononitrile and fumaronitrile in vitro. These dinitriles are converted to the corresponding monoacid mononitriles, showing the enzyme is regioselective. Cannot hydrolyze compounds with a nitrile group bound to an aromatic ring or amino acid. Its biological role is unknown.<ref>PMID:16495079</ref> | ||
| + | == 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/3ivz_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/main_output.php?pdb_ID=3ivz ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The nitrilase superfamily is a large and diverse superfamily of enzymes that catalyse the cleavage of various types of carbon-nitrogen bonds using a Cys-Glu-Lys catalytic triad. Thermoactive nitrilase from Pyrococcus abyssi (PaNit) hydrolyses small aliphatic nitriles like fumaro- and malononitryl. Yet, the biological role of this enzyme is unknown. We have analysed several crystal structures of PaNit: without ligands, with an acetate ion bound in the active site and with a bromide ion in the active site. In addition, docking calculations have been performed for fumaro- and malononitriles. The structures provide a proof for specific binding of the carboxylate ion and a general affinity for negatively changed ligands. The role of residues in the active site is considered and an enzymatic reaction mechanism is proposed in which Cys146 acts as the nucleophile, Glu42 as the general base, Lys113/Glu42 as the general acid, WatA as the hydrolytic water and Nzeta_Lys113 and N_Phe147 form the oxyanion hole. | ||
| - | + | Crystallographic analysis of a thermoactive nitrilase.,Raczynska JE, Vorgias CE, Antranikian G, Rypniewski W J Struct Biol. 2011 Feb;173(2):294-302. Epub 2010 Nov 21. PMID:21095228<ref>PMID:21095228</ref> | |
| - | <ref | + | |
| - | [[Category: | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | [[Category: Pyrococcus abyssi]] | + | </div> |
| - | [[Category: Antranikian | + | <div class="pdbe-citations 3ivz" style="background-color:#fffaf0;"></div> |
| - | [[Category: Raczynska | + | == References == |
| - | [[Category: Rypniewski | + | <references/> |
| - | [[Category: Vorgias | + | __TOC__ |
| - | + | </StructureSection> | |
| - | + | [[Category: Large Structures]] | |
| + | [[Category: Pyrococcus abyssi GE5]] | ||
| + | [[Category: Antranikian G]] | ||
| + | [[Category: Raczynska J]] | ||
| + | [[Category: Rypniewski W]] | ||
| + | [[Category: Vorgias C]] | ||
Current revision
Crystal structure of hyperthermophilic nitrilase
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