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| | <StructureSection load='3a8m' size='340' side='right'caption='[[3a8m]], [[Resolution|resolution]] 1.32Å' scene=''> | | <StructureSection load='3a8m' size='340' side='right'caption='[[3a8m]], [[Resolution|resolution]] 1.32Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a8m]] 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=3A8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A8M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a8m]] 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=3A8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A8M 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]] 1.32Å</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></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=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;'>[[3a8g|3a8g]], [[3a8h|3a8h]], [[3a8l|3a8l]], [[3a8o|3a8o]]</div></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=3a8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a8m OCA], [https://pdbe.org/3a8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a8m RCSB], [https://www.ebi.ac.uk/pdbsum/3a8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a8m 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=3a8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a8m OCA], [https://pdbe.org/3a8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a8m RCSB], [https://www.ebi.ac.uk/pdbsum/3a8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a8m 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. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a8/3a8m_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a8/3a8m_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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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: Ohtaki, A]] | + | [[Category: Ohtaki A]] |
| - | [[Category: Yamanaka, Y]] | + | [[Category: Yamanaka Y]] |
| - | [[Category: Yohda, M]] | + | [[Category: Yohda M]] |
| - | [[Category: Fe]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxidation]]
| + | |
| Structural highlights
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.
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
Nitrile hydratases (NHase), which catalyze the hydration of nitriles to amides, have an unusual Fe(3+) or Co(3+) center with two modified Cys ligands: cysteine sulfininate (Cys-SO(2) (-)) and either cysteine sulfenic acid or cysteine sulfenate [Cys-SO(H)]. Two catalytic mechanisms have been proposed. One is that the sulfenyl oxygen activates a water molecule, enabling nucleophilic attack on the nitrile carbon. The other is that the Ser ligand ionizes the strictly conserved Tyr, activating a water molecule. Here, we characterized mutants of Fe-type NHase from Rhodococcus erythropolis N771, replacing the Ser and Tyr residues, alphaS113A and betaY72F. The alphaS113A mutation partially affected catalytic activity and did not change the pH profiles of the kinetic parameters. UV-vis absorption spectra indicated that the electronic state of the Fe center was altered by the alphaS113A mutation, but the changes could be prevented by a competitive inhibitor, n-butyric acid. The overall structure of the alphaS113A mutant was similar to that of the wild type, but significant changes were observed around the catalytic cavity. Like the UV-vis spectra, the changes were compensated by the substrate or product. The Ser ligand is important for the structure around the catalytic cavity, but is not essential for catalysis. The betaY72F mutant exhibited no activity. The structure of the betaY72F mutant was highly conserved but was found to be the inactivated state, with alphaCys114-SO(H) oxidized to Cys-SO(2) (-), suggesting that betaTyr72 affected the electronic state of the Fe center. The catalytic mechanism is discussed on the basis of the results obtained.
Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase.,Yamanaka Y, Hashimoto K, Ohtaki A, Noguchi K, Yohda M, Odaka M J Biol Inorg Chem. 2010 Mar 10. PMID:20221653[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yamanaka Y, Hashimoto K, Ohtaki A, Noguchi K, Yohda M, Odaka M. Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase. J Biol Inorg Chem. 2010 Mar 10. PMID:20221653 doi:10.1007/s00775-010-0632-3
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