6OND

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

Summary for 6OND

• Entry DOI: 10.2210/pdb6ond/pdb
• Descriptor: Carbon monoxide dehydrogenase, IRON/SULFUR CLUSTER, FE(4)-NI(1)-S(4) CLUSTER, ... (9 entities in total)
• Functional Keywords: nickel-iron-sulfur (ni-fe-s) cluster, iron-sulfur (fe-s) cluster, metalloenzyme, oxidoreductase
• Biological source: Desulfovibrio vulgaris
• Total number of polymer chains: 4
• Total formula weight: 274926.00

Authors

Wittenborn, E.C.,Cohen, S.E.,Drennan, C.L. (deposition date: 2019-04-21, release date: 2019-07-24, Last modification date: 2023-10-11)

Primary citation

Wittenborn, E.C.,Cohen, S.E.,Merrouch, M.,Leger, C.,Fourmond, V.,Dementin, S.,Drennan, C.L.
Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase.
J.Biol.Chem., 294:13017-13026, 2019

PubMed Abstract: The nickel-dependent carbon monoxide dehydrogenase (CODH) employs a unique heterometallic nickel-iron-sulfur cluster, termed the C-cluster, to catalyze the interconversion of CO and CO 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 Å resolution) of CODH from (CODH) heterologously expressed in either the absence (CODH) or presence (CODH) of co-expressed CooC. We find that the C-cluster of CODH is fully loaded with iron but does not contain any nickel. Interestingly, the so-called unique iron ion (Fe) 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 CODH variant that lacks a surface-accessible iron-sulfur 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 Fe is in its canonical location, and the nickel site is empty. This D-cluster-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 C-cluster assembly that requires both CooC and a functioning D-cluster, involves precise redox-state control, and includes a two-step nickel-binding process.

PubMed: 31296570
DOI: 10.1074/jbc.RA119.009610

Experimental method

X-RAY DIFFRACTION (1.723 Å)