6ond

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, reduced

Structural highlights

6ond is a 4 chain structure with sequence from Desulfovibrio vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.723Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q72A99_DESVH

Publication Abstract from PubMed

The nickel-dependent carbon monoxide dehydrogenase (CODH) employs a unique heterometallic Ni-Fe-S cluster, termed the Ccluster, to catalyze the interconversion of CO and CO2 Like other complex metalloenzymes, CODH requires dedicated assembly machinery to form the fully intact and functional C-cluster. In particular, nickel incorporation into the C-cluster depends on the maturation factor CooC; however, the mechanism of nickel insertion remains poorly understood. Here, we compare X-ray structures (1.50-2.48 A resolution) of CODH from Desulfovibrio vulgaris (DvCODH) heterologously expressed in either the absence (DvCODH(-CooC)) or presence (DvCODH(+CooC)) of co-expressed CooC. We find that the C-cluster of DvCODH(-CooC) is fully loaded with iron but does not contain any nickel. Interestingly, the so-called unique iron ion (Feu) occupies both its canonical site (80% occupancy) and the nickel site (20% occupancy), with addition of reductant causing further mismetallation of the nickel site (60% iron occupancy). We also demonstrate that a DvCODH variant that lacks a surface-accessible Fe-S cluster (the D-cluster) has a C-cluster that is also replete in iron but lacks nickel, despite co-expression with CooC. In this variant, all Feu is in its canonical location and the nickel site is empty. This Dcluster-deficient CODH is inactive despite attempts to reconstitute it with nickel. Taken together, these results suggest that an empty nickel site is not sufficient for nickel incorporation. Based on our findings, we propose a model for Ccluster assembly that requires both CooC and a functioning D-cluster, involves precise redox-state control, and includes a two-step nickel-binding process.

Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase.,Wittenborn EC, Cohen SE, Merrouch M, Leger C, Fourmond V, Dementin S, Drennan CL J Biol Chem. 2019 Jul 11. pii: RA119.009610. doi: 10.1074/jbc.RA119.009610. PMID:31296570^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wittenborn EC, Cohen SE, Merrouch M, Leger C, Fourmond V, Dementin S, Drennan CL. Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase. J Biol Chem. 2019 Jul 11. pii: RA119.009610. doi: 10.1074/jbc.RA119.009610. PMID:31296570 doi:http://dx.doi.org/10.1074/jbc.RA119.009610

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ond"

Categories: Desulfovibrio vulgaris | Large Structures | Cohen SE | Drennan CL | Wittenborn EC

@@ Line 3: / Line 3: @@
 <StructureSection load='6ond' size='340' side='right'caption='[[6ond]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ond]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OND FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ond]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OND FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=XCC:FE(4)-NI(1)-S(4)+CLUSTER'>XCC</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]] 1.723&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Anaerobic_carbon-monoxide_dehydrogenase Anaerobic carbon-monoxide dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.4 1.2.7.4] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=XCC:FE(4)-NI(1)-S(4)+CLUSTER'>XCC</scene></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=6ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ond OCA], [http://pdbe.org/6ond PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ond RCSB], [http://www.ebi.ac.uk/pdbsum/6ond PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ond 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=6ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ond OCA], [https://pdbe.org/6ond PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ond RCSB], [https://www.ebi.ac.uk/pdbsum/6ond PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ond ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q72A99_DESVH Q72A99_DESVH]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 6ond" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Anaerobic carbon-monoxide dehydrogenase]]
+[[Category: Desulfovibrio vulgaris]]
 [[Category: Large Structures]]
-[[Category: Cohen, S E]]
+[[Category: Cohen SE]]
-[[Category: Drennan, C L]]
+[[Category: Drennan CL]]
-[[Category: Wittenborn, E C]]
+[[Category: Wittenborn EC]]
-[[Category: Metalloenzyme]]
-[[Category: Oxidoreductase]]

6ond

From Proteopedia

Current revision

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, reduced

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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