2zpe: Difference between revisions

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-{{Seed}}
-[[Image:2zpe.png|left|200px]]
-<!--
+==nitrosylated Fe-type nitrile hydratase with tert-butylisonitrile==
-The line below this paragraph, containing "STRUCTURE_2zpe", creates the "Structure Box" on the page.
+<StructureSection load='2zpe' size='340' side='right'caption='[[2zpe]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2zpe]] 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=2ZPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZPE FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.48&#8491;</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=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=TB0:TERT-BUTYL+ISOCYANIDE'>TB0</scene></td></tr>
-{{STRUCTURE_2zpe|  PDB=2zpe  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zpe OCA], [https://pdbe.org/2zpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zpe RCSB], [https://www.ebi.ac.uk/pdbsum/2zpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zpe ProSAT]</span></td></tr>
+</table>
+== 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.
+== 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/2zpe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2zpe 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.
-===nitrosylated Fe-type nitrile hydratase with tert-butylisonitrile===
+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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zpe" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18948265}}, adds the Publication Abstract to the page
+*[[Nitrile hydratase|Nitrile hydratase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18948265 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18948265}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-ZPE is a 2 chains structure of sequences 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=2ZPE OCA].
-==Reference==
-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 Oct 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18948265 18948265]
-[[Category: Nitrile hydratase]]
 [[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 17 13:03:58 2008''