3a8o: Difference between revisions
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==Crystal structure of Nitrile Hydratase complexed with Trimethylacetamide== | |||
=== | <StructureSection load='3a8o' size='340' side='right' caption='[[3a8o]], [[Resolution|resolution]] 1.47Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3a8o]] is a 2 chain structure with sequence from [http://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=3A8O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A8O FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=TAY:2,2-DIMETHYLPROPANAMIDE'>TAY</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a8g|3a8g]], [[3a8h|3a8h]], [[3a8l|3a8l]], [[3a8m|3a8m]]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3a8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a8o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3a8o RCSB], [http://www.ebi.ac.uk/pdbsum/3a8o 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/a8/3a8o_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 (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<ref>PMID:20221653</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: Mycobacterium erythropolis gray and thornton 1928]] | [[Category: Mycobacterium erythropolis gray and thornton 1928]] | ||
[[Category: Nitrile hydratase]] | [[Category: Nitrile hydratase]] | ||
[[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: Fe]] | ||
[[Category: Iron]] | [[Category: Iron]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Metal-binding]] | [[Category: Metal-binding]] | ||
[[Category: Oxidation]] | [[Category: Oxidation]] | ||
Revision as of 19:44, 21 December 2014
Crystal structure of Nitrile Hydratase complexed with TrimethylacetamideCrystal structure of Nitrile Hydratase complexed with Trimethylacetamide
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 (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 AlsoReferences
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