2zpi: Difference between revisions
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[[Image: | ==Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 440min at 293K== | ||
<StructureSection load='2zpi' size='340' side='right' caption='[[2zpi]], [[Resolution|resolution]] 1.49Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2zpi]] 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=2ZPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZPI FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br> | |||
<tr><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><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]], [[2zph|2zph]]</td></tr> | |||
<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zpi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zpi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zpi RCSB], [http://www.ebi.ac.uk/pdbsum/2zpi PDBsum]</span></td></tr> | |||
<table> | |||
== 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/zp/2zpi_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:18948265</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | |||
*[[Nitrile hydratase|Nitrile hydratase]] | |||
== | == References == | ||
[[ | <references/> | ||
__TOC__ | |||
== | </StructureSection> | ||
< | |||
[[Category: Nitrile hydratase]] | [[Category: Nitrile hydratase]] | ||
[[Category: Rhodococcus erythropolis]] | [[Category: Rhodococcus erythropolis]] | ||
Revision as of 08:19, 2 October 2014
Complex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 440min at 293KComplex of Fe-type nitrile hydratase with tert-butylisonitrile, photo-activated for 440min at 293K
Structural highlights
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 PubMedNitrile 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 AlsoReferences
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