This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1jqk

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:41, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1jqk.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum==
-
|PDB= 1jqk |SIZE=350|CAPTION= <scene name='initialview01'>1jqk</scene>, resolution 2.8&Aring;
+
<StructureSection load='1jqk' size='340' side='right'caption='[[1jqk]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=WCC:FE(3)-NI(1)-S(4)+CLUSTER'>WCC</scene>
+
<table><tr><td colspan='2'>[[1jqk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JQK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQK FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[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] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=WCC:FE(3)-NI(1)-S(4)+CLUSTER'>WCC</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqk OCA], [https://pdbe.org/1jqk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jqk RCSB], [https://www.ebi.ac.uk/pdbsum/1jqk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jqk ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jqk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jqk OCA], [http://www.ebi.ac.uk/pdbsum/1jqk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jqk RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/COOS_RHORU COOS_RHORU] Allows growth in a CO-dependent manner in the dark. CODH oxidizes carbon monoxide coupled, via CooF, to the reduction of a hydrogen cation by a hydrogenase (possibly CooH).
 +
== 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/jq/1jqk_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=1jqk ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum'''
+
==See Also==
-
 
+
*[[Carbon monoxide dehydrogenase|Carbon monoxide dehydrogenase]]
-
 
+
*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
-
==Overview==
+
*[[Iron–sulfur proteins|Iron–sulfur proteins]]
-
A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-A resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe(3)S(4)] and not [Fe(4)S(4)]. The mononuclear site and the four-metal cluster are bridged by means of Cys(531) and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe(4)S(4)] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an alpha/beta (Rossmann-like) domain in the middle, and an alpha/beta (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe(4)S(4)] cluster and another [Fe(4)S(4)] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems.
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
1JQK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodospirillum_rubrum Rhodospirillum rubrum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JQK OCA].
+
-
 
+
-
==Reference==
+
-
Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase., Drennan CL, Heo J, Sintchak MD, Schreiter E, Ludden PW, Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):11973-8. Epub 2001 Oct 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11593006 11593006]
+
-
[[Category: Carbon-monoxide dehydrogenase (acceptor)]]
+
[[Category: Rhodospirillum rubrum]]
[[Category: Rhodospirillum rubrum]]
-
[[Category: Single protein]]
+
[[Category: Drennan CL]]
-
[[Category: Drennan, C L.]]
+
[[Category: Heo J]]
-
[[Category: Heo, J.]]
+
[[Category: Ludden PW]]
-
[[Category: Ludden, P W.]]
+
[[Category: Schreiter E]]
-
[[Category: Schreiter, E.]]
+
[[Category: Sintchak MD]]
-
[[Category: Sintchak, M D.]]
+
-
[[Category: rossmann fold]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:37:31 2008''
+

Current revision

Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum

PDB ID 1jqk

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1jqk"
Personal tools