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| | <StructureSection load='3wvd' size='340' side='right'caption='[[3wvd]], [[Resolution|resolution]] 1.18Å' scene=''> | | <StructureSection load='3wvd' size='340' side='right'caption='[[3wvd]], [[Resolution|resolution]] 1.18Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wvd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WVD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wvd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WVD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAN:2,2-DIMETHYLPROPANENITRILE'>TAN</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]] 1.18Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAN:2,2-DIMETHYLPROPANENITRILE'>TAN</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;'>[[3wve|3wve]]</div></td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nthA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 "Mycobacterium erythropolis" Gray and Thornton 1928]), nthB, nha2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 "Mycobacterium erythropolis" Gray and Thornton 1928])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrile_hydratase Nitrile hydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.84 4.2.1.84] </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=3wvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wvd OCA], [https://pdbe.org/3wvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wvd RCSB], [https://www.ebi.ac.uk/pdbsum/3wvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wvd 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=3wvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wvd OCA], [https://pdbe.org/3wvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wvd RCSB], [https://www.ebi.ac.uk/pdbsum/3wvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wvd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NHAA_RHOER NHAA_RHOER]] NHase catalyzes the hydration of various nitrile compounds to the corresponding amides. Industrial production of acrylamide is now being developed using some of the enzymes of this class. [[https://www.uniprot.org/uniprot/NHAB_RHOER NHAB_RHOER]] NHase catalyzes the hydration of various nitrile compounds to the corresponding amides.
| + | [https://www.uniprot.org/uniprot/NHAA_RHOER NHAA_RHOER] NHase catalyzes the hydration of various nitrile compounds to the corresponding amides. Industrial production of acrylamide is now being developed using some of the enzymes of this class. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Mycobacterium erythropolis gray and thornton 1928]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nitrile hydratase]] | + | [[Category: Rhodococcus erythropolis]] |
| - | [[Category: Hashimoto, K]] | + | [[Category: Hashimoto K]] |
| - | [[Category: Noguchi, K]] | + | [[Category: Noguchi K]] |
| - | [[Category: Odaka, M]] | + | [[Category: Odaka M]] |
| - | [[Category: Yamanaka, Y]] | + | [[Category: Yamanaka Y]] |
| - | [[Category: Yohda, M]] | + | [[Category: Yohda M]] |
| - | [[Category: Cys-so2h]]
| + | |
| - | [[Category: Cys-soh]]
| + | |
| - | [[Category: Cysteine sulfinic acid]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
3wvd is a 2 chain structure with sequence from Rhodococcus erythropolis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.18Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
NHAA_RHOER NHase catalyzes the hydration of various nitrile compounds to the corresponding amides. Industrial production of acrylamide is now being developed using some of the enzymes of this class.
Publication Abstract from PubMed
The reaction mechanism of nitrile hydratase (NHase) was investigated using time-resolved crystallography of the mutant NHase, in which betaArg56, strictly conserved and hydrogen bonded to the two post-translationally oxidized cysteine ligands, was replaced by lysine, and pivalonitrile was the substrate. The crystal structures of the reaction intermediates were determined at high resolution (1.2-1.3 A). In combination with FTIR analyses of NHase following hydration in H2 (18) O, we propose that the metal-coordinated substrate is nucleophilically attacked by the O(SO(-) ) atom of alphaCys114-SO(-) , followed by nucleophilic attack of the S(SO(-) ) atom by a betaArg56-activated water molecule to release the product amide and regenerate alphaCys114-SO(-) .
Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile.,Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10763-7. doi: 10.1002/anie.201502731. PMID:26333053[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yamanaka Y, Kato Y, Hashimoto K, Iida K, Nagasawa K, Nakayama H, Dohmae N, Noguchi K, Noguchi T, Yohda M, Odaka M. Time-Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile. Angew Chem Int Ed Engl. 2015 Sep 7;54(37):10763-7. doi: 10.1002/anie.201502731. PMID:26333053 doi:http://dx.doi.org/10.1002/anie.201502731
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