|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='2zph' size='340' side='right'caption='[[2zph]], [[Resolution|resolution]] 1.59Å' scene=''> | | <StructureSection load='2zph' size='340' side='right'caption='[[2zph]], [[Resolution|resolution]] 1.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZPH OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2ZPH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zph]] 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=2ZPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZPH 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=TB0:TERT-BUTYL+ISOCYANIDE'>TB0</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.59Å</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=TB0:TERT-BUTYL+ISOCYANIDE'>TB0</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ahj|2ahj]], [[2cz6|2cz6]], [[2cz7|2cz7]], [[2d0q|2d0q]], [[2zpb|2zpb]], [[2zpe|2zpe]], [[2zpf|2zpf]], [[2zpg|2zpg]], [[2zpi|2zpi]]</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=2zph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zph OCA], [https://pdbe.org/2zph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zph RCSB], [https://www.ebi.ac.uk/pdbsum/2zph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zph ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrile_hydratase Nitrile hydratase], with EC number [http://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'>[http://proteopedia.org/fgij/fg.htm?mol=2zph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zph OCA], [http://pdbe.org/2zph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zph RCSB], [http://www.ebi.ac.uk/pdbsum/2zph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zph ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. [[http://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]] |
| Line 17: |
Line 15: |
| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zp/2zph_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zp/2zph_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> |
| Line 39: |
Line 37: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nitrile hydratase]] | |
| | [[Category: Rhodococcus erythropolis]] | | [[Category: Rhodococcus erythropolis]] |
| - | [[Category: Hashimoto, K]] | + | [[Category: Hashimoto K]] |
| - | [[Category: Noguchi, T]] | + | [[Category: Noguchi T]] |
| - | [[Category: Odaka, M]] | + | [[Category: Odaka M]] |
| - | [[Category: Suzuki, H]] | + | [[Category: Suzuki H]] |
| - | [[Category: Taniguchi, K]] | + | [[Category: Taniguchi K]] |
| - | [[Category: Yohda, M]] | + | [[Category: Yohda M]] |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxidation]]
| + | |
| Structural highlights
2zph 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 1.59Å |
| 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.
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 (NHases) have an unusual iron or cobalt catalytic center with two oxidized cysteine ligands, cysteine-sulfinic acid and cysteine-sulfenic acid, catalyzing the hydration of nitriles to amides. Recently, we found that the NHase of Rhodococcus erythropolis N771 exhibited an additional catalytic activity, converting tert-butylisonitrile (tBuNC) to tert-butylamine. Taking advantage of the slow reactivity of tBuNC and the photoreactivity of nitrosylated NHase, we present the first structural evidence for the catalytic mechanism of NHase with time-resolved x-ray crystallography. By monitoring the reaction with attenuated total reflectance-Fourier transform infrared spectroscopy, the product from the isonitrile carbon was identified as a CO molecule. Crystals of nitrosylated inactive NHase were soaked with tBuNC. The catalytic reaction was initiated by photo-induced denitrosylation and stopped by flash cooling. tBuNC was first trapped at the hydrophobic pocket above the iron center and then coordinated to the iron ion at 120 min. At 440 min, the electron density of tBuNC was significantly altered, and a new electron density was observed near the isonitrile carbon as well as the sulfenate oxygen of alphaCys114. These results demonstrate that the substrate was coordinated to the iron and then attacked by a solvent molecule activated by alphaCys114-SOH.
Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile.,Hashimoto K, Suzuki H, Taniguchi K, Noguchi T, Yohda M, Odaka M J Biol Chem. 2008 Dec 26;283(52):36617-23. Epub 2008 Oct 23. PMID:18948265[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hashimoto K, Suzuki H, Taniguchi K, Noguchi T, Yohda M, Odaka M. Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile. J Biol Chem. 2008 Dec 26;283(52):36617-23. Epub 2008 Oct 23. PMID:18948265 doi:10.1074/jbc.M806577200
|
