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| | <StructureSection load='3ivz' size='340' side='right'caption='[[3ivz]], [[Resolution|resolution]] 1.57Å' scene=''> | | <StructureSection load='3ivz' size='340' side='right'caption='[[3ivz]], [[Resolution|resolution]] 1.57Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ivz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrab Pyrab]. 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> | + | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3iw3|3iw3]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nit-30, PAB1449, PYRAB13990 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-ureidopropionase Beta-ureidopropionase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.6 3.5.1.6] </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=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> | | <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> | | </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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-ureidopropionase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrab]] | + | [[Category: Pyrococcus abyssi GE5]] |
| - | [[Category: Antranikian, G]] | + | [[Category: Antranikian G]] |
| - | [[Category: Raczynska, J]] | + | [[Category: Raczynska J]] |
| - | [[Category: Rypniewski, W]] | + | [[Category: Rypniewski W]] |
| - | [[Category: Vorgias, C]] | + | [[Category: Vorgias C]] |
| - | [[Category: Alpha-beta sandwich]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
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.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mueller P, Egorova K, Vorgias CE, Boutou E, Trauthwein H, Verseck S, Antranikian G. Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi. Protein Expr Purif. 2006 Jun;47(2):672-81. PMID:16495079 doi:10.1016/j.pep.2006.01.006
- ↑ Raczynska JE, Vorgias CE, Antranikian G, Rypniewski W. Crystallographic analysis of a thermoactive nitrilase. J Struct Biol. 2011 Feb;173(2):294-302. Epub 2010 Nov 21. PMID:21095228 doi:10.1016/j.jsb.2010.11.017
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