6onc

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(Difference between revisions)

Revision as of 11:54, 1 January 2020

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, as-isolated

Structural highlights

6onc is a 4 chain structure with sequence from Atcc 29579. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , ,
Gene:	cooS, DVU_2098 (ATCC 29579)
Activity:	Anaerobic carbon-monoxide dehydrogenase, with EC number 1.2.7.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='6onc' size='340' side='right'caption='[[6onc]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6onc]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ONC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ONC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6onc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ONC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ONC 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>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cooS, DVU_2098 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=881 ATCC 29579])</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='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=6onc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6onc OCA], [http://pdbe.org/6onc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6onc RCSB], [http://www.ebi.ac.uk/pdbsum/6onc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6onc ProSAT]</span></td></tr>
@@ Line 22: / Line 23: @@
 </StructureSection>
 [[Category: Anaerobic carbon-monoxide dehydrogenase]]
+[[Category: Atcc 29579]]
 [[Category: Large Structures]]
 [[Category: Cohen, S E]]

6onc

From Proteopedia

Revision as of 11:54, 1 January 2020

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, as-isolated

Structural highlights

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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