1n63: Difference between revisions

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-[[Image:1n63.gif|left|200px]]<br /><applet load="1n63" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1n63, resolution 1.21&Aring;" />
-'''Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Carbon monoxide reduced state'''<br />
-==Overview==
+==Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Carbon monoxide reduced state==
-The CO dehydrogenase of the eubacterium Oligotropha carboxidovorans is a, 277-kDa Mo- and Cu-containing iron-sulfur flavoprotein. Here, the enzyme's, active site in the oxidized or reduced state, after inactivation with, potassium cyanide or with n-butylisocyanide bound to the active site, has, been reinvestigated by multiple wavelength anomalous dispersion, measurements at atomic resolution, electron spin resonance spectroscopy, and chemical analyses. We present evidence for a dinuclear heterometal, [CuSMoO)OH] cluster in the active site of the oxidized or reduced enzyme, which is prone to cyanolysis. The cluster is coordinated through, interactions of the Mo with the dithiolate pyran ring of molybdopterin, cytosine dinucleotide and of the Cu with the Sgamma of Cys-388, which is, part of the active-site loop VAYRC(388)SFR. The previously reported, active-site structure [Dobbek, H., Gremer, L., Meyer, O. &amp; Huber, R., (1999) Proc. Natl. Acad. Sci. USA 96, 8884-8889] of an Mo with three, oxygen ligands and an SeH-group bound to the Sgamma atom of Cys-388 could, not be confirmed. The structure of CO dehydrogenase with the inhibitor, n-butylisocyanide bound has led to a model for the catalytic mechanism of, CO oxidation which involves a thiocarbonate-like intermediate state. The, dinuclear [CuSMo(O)OH] cluster of CO dehydrogenase establishes a, previously uncharacterized class of dinuclear molybdoenzymes containing, the pterin cofactor.
+<StructureSection load='1n63' size='340' side='right'caption='[[1n63]], [[Resolution|resolution]] 1.21&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1n63]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Afipia_carboxidovorans_OM5 Afipia carboxidovorans OM5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N63 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.21&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CUN:CU(I)-S-MO(IV)(=O)OH+CLUSTER'>CUN</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MCN:PTERIN+CYTOSINE+DINUCLEOTIDE'>MCN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=1n63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n63 OCA], [https://pdbe.org/1n63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n63 RCSB], [https://www.ebi.ac.uk/pdbsum/1n63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n63 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DCMS_AFIC5 DCMS_AFIC5] Catalyzes the oxidation of carbon monoxide to carbon dioxide.<ref>PMID:12475995</ref> <ref>PMID:21275368</ref>
+== 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/n6/1n63_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/main_output.php?pdb_ID=1n63 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-N63 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Oligotropha_carboxidovorans Oligotropha carboxidovorans] with PO4, FES, CUN, MCN and FAD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.2 1.2.99.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N63 OCA].
+*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution., Dobbek H, Gremer L, Kiefersauer R, Huber R, Meyer O, Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15971-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12475995 12475995]
+__TOC__
-[[Category: Carbon-monoxide dehydrogenase (acceptor)]]
+</StructureSection>
-[[Category: Oligotropha carboxidovorans]]
+[[Category: Afipia carboxidovorans OM5]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Dobbek, H.]]
+[[Category: Dobbek H]]
-[[Category: Gremer, L.]]
+[[Category: Gremer L]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Kiefersauer, R.]]
+[[Category: Kiefersauer R]]
-[[Category: Meyer, O.]]
+[[Category: Meyer O]]
-[[Category: CUN]]
-[[Category: FAD]]
-[[Category: FES]]
-[[Category: MCN]]
-[[Category: PO4]]
-[[Category: codh]]
-[[Category: copper]]
-[[Category: molybdenum]]
-[[Category: molybdopterin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:59:41 2007''