1n63: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='1n63' size='340' side='right'caption='[[1n63]], [[Resolution|resolution]] 1.21&Aring;' scene=''>
<StructureSection load='1n63' size='340' side='right'caption='[[1n63]], [[Resolution|resolution]] 1.21&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1n63]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligotropha_carboxidovorans Oligotropha carboxidovorans]. 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>
<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='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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n5w|1n5w]], [[1n60|1n60]], [[1n61|1n61]], [[1n62|1n62]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.2 1.2.99.2] </span></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>
<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>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DCMS_OLICO DCMS_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[https://www.uniprot.org/uniprot/DCMM_OLICO DCMM_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide. [[https://www.uniprot.org/uniprot/DCML_OLICO DCML_OLICO]] Catalyzes the oxidation of carbon monoxide to carbon dioxide.
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 21: Line 20:
</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:12475995<ref>PMID:12475995</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1n63" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 37: Line 27:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Afipia carboxidovorans OM5]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Oligotropha carboxidovorans]]
[[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: Codh]]
[[Category: Molybdenum]]
[[Category: Molybdopterin]]
[[Category: Oxidoreductase]]

Latest revision as of 16:27, 13 March 2024

Crystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Carbon monoxide reduced stateCrystal Structure of the Cu,Mo-CO Dehydrogenase (CODH); Carbon monoxide reduced state

Structural highlights

1n63 is a 6 chain structure with sequence from Afipia carboxidovorans OM5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.21Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCMS_AFIC5 Catalyzes the oxidation of carbon monoxide to carbon dioxide.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Dobbek H, Gremer L, Kiefersauer R, Huber R, Meyer O. Catalysis at a dinuclear [CuSMo(==O)OH] cluster in a CO dehydrogenase resolved at 1.1-A resolution. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15971-6. PMID:12475995 doi:10.1073/pnas.212640899
  2. ↑ Wilcoxen J, Zhang B, Hille R. Reaction of the molybdenum from Oligotropha carboxydovorans with quinones. Biochemistry. 2011 Mar 22;50(11):1910-6. PMID:21275368 doi:10.1021/bi1017182

1n63, resolution 1.21Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1n63&oldid=4087510"