Maturation of the [Ni–4Fe–4S] active site of carbon monoxide dehydrogenases

Merrouch, Mériem; Benvenuti, M.; Lorenzi, Marco; Léger, Christophe; Fourmond, Vincent; Dementin, Sébastien

doi:10.1007/s00775-018-1541-0

Cited by 24 publications

(16 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Two conserved cysteines from each monomer are involved in Ni coordination [36]. That the CODH produced in the absence of CooC cannot be activated by exogenous Ni shows that CooC is not just involved in the delivery of the metal, but also in the preparation of the active site for receiving the nickel [37] This is consistent with our previous investigation of Dv CODH [18,30]. Our data show that the CODHs matured in the presence of either CooC1 or CooC2, which share ~ 40 % identity (SI Figure S9), have similar values of activity and nickel content.…”

Section: Discussionmentioning

confidence: 99%

The two CO-dehydrogenases of Thermococcus sp. AM4

Benvenuti

Meneghello

Guendon

et al. 2020

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Self Cite

View full text Add to dashboard Cite

Ni-containing CO-dehydrogenases (CODHs) allow some microorganisms to couple ATP synthesis to CO oxidation, or to use either CO or CO 2 as a source of carbon. The recent detailed characterizations of some of them has evidenced a great diversity in terms of catalytic properties and resistance to O 2. In an effort to increase the number of available CODHs, we have heterologously produced in Desulfovibrio fructosovorans, purified and characterized the two CooS-type CODHs (CooS1 and CooS2) from the hyperthermophilic archaeon Thermococcus sp. AM4 (Tc). We have also crystallized CooS2, which is coupled in vivo to a hydrogenase. CooS1 and CooS2 are homodimers, and harbour five metalloclusters: two NiFe 4 S 4 C clusters, two [4Fe4S] B clusters and one interfacial [4Fe4S] D cluster. We show that both are dependent on a maturase, CooC1 or CooC2, which is interchangeable. The homologous protein CooC3 does not allow Ni insertion in either CooS. The two CODHs from Tc have similar properties: they can both oxidize and produce CO. The Michaelis constants (K m) are in the microM range for CO and in the mM range (CODH 1) or above (CODH 2) for CO 2. Product inhibition is observed only for CO 2 reduction, consistent with CO 2 binding being much weaker than CO binding. The two enzymes are rather O 2 sensitive (similarly to CODH II from Carboxydothermus hydrogenoformans), and react more slowly with O 2 than any other CODH for which these data are available.

show abstract

Section: Discussionmentioning

confidence: 99%

The two CO-dehydrogenases of Thermococcus sp. AM4

Benvenuti

Meneghello

Guendon

et al. 2020

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Self Cite

View full text Add to dashboard Cite

show abstract

“…The MRP-MinD subfamily of P-loop NTPases containing Cfd1 and Nbp35 encompasses a number of other archaeal and bacterial members that are involved in metal center assembly, but their primary sequences are homologous to Cfd1-Nbp35 only within the Walker region. For example, CooC1 assists the maturation of the Ni-containing carbon monoxide dehydrogenase (CODH) (70,71). Two monomers transiently bind a Ni 2+ ion in a bridging fashion and presumably transfer it to CODH in an ATP-dependent fashion.…”

Section: Discussionmentioning

confidence: 99%

Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins

Stehling

Jeoung

Freibert

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Maturation of iron-sulfur (Fe-S) proteins in eukaryotes requires complex machineries in mitochondria and cytosol. Initially, Fe-S clusters are assembled on dedicated scaffold proteins and then are trafficked to target apoproteins. Within the cytosolic Fe-S protein assembly (CIA) machinery, the conserved P-loop nucleoside triphosphatase Nbp35 performs a scaffold function. In yeast, Nbp35 cooperates with the related Cfd1, which is evolutionary less conserved and is absent in plants. Here, we investigated the potential scaffold function of human CFD1 (NUBP2) in CFD1-depleted HeLa cells by measuring Fe-S enzyme activities or Fe incorporation into Fe-S target proteins. We show that CFD1, in complex with NBP35 (NUBP1), performs a crucial role in the maturation of all tested cytosolic and nuclear Fe-S proteins, including essential ones involved in protein translation and DNA maintenance. CFD1 also matures iron regulatory protein 1 and thus is critical for cellular iron homeostasis. To better understand the scaffold function of CFD1-NBP35, we resolved the crystal structure of holo-Cfd1 (ctCfd1) at 2.6-Å resolution as a model Cfd1 protein. Importantly, two ctCfd1 monomers coordinate a bridging [4Fe-4S] cluster via two conserved cysteine residues. The surface-exposed topology of the cluster is ideally suited for both de novo assembly and facile transfer to Fe-S apoproteins mediated by other CIA factors. ctCfd1 specifically interacted with ATP, which presumably associates with a pocket near the Cfd1 dimer interface formed by the conserved Walker motif. In contrast, ctNbp35 preferentially bound GTP, implying differential regulation of the two fungal scaffold components during Fe-S cluster assembly and/or release.

show abstract

“…In analogy to UreG and HypB, CooC has been proposed to use ATP hydrolysis to facilitate nickel insertion into CODH (15,16,23,24). Alternatively, CooC has been proposed to fold or otherwise mediate formation of the proper nickel binding site in CODH (16,17,25).…”

Section: Introductionmentioning

confidence: 99%

“…Incubation of the as-isolated DvCODH +CooC with both NiCl2 and the reductant sodium dithionite results in elimination of the lag phase and a 10-fold increase in CO oxidation activity; however, activation does not occur in the presence of NiCl2 or sodium dithionite alone (17). In contrast, as-isolated DvCODH −CooC contains low amounts of nickel (0-0.2 Ni/monomer), has nearly no activity (4% of asisolated DvCODH +CooC ), and undergoes limited activation with NiCl2 and sodium dithionite (17), suggesting that DvCooC is involved in constructing the appropriate nickel binding site in DvCODH (25).…”

Section: Introductionmentioning

confidence: 99%

Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase

Wittenborn

Cohen

Merrouch

et al. 2019

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The nickel-dependent carbon monoxide dehydrogenase (CODH) employs a unique heterometallic Ni-Fe-S cluster, termed the C-cluster, 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 Å 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 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.

show abstract

Maturation of the [Ni–4Fe–4S] active site of carbon monoxide dehydrogenases

Cited by 24 publications

References 60 publications

The two CO-dehydrogenases of Thermococcus sp. AM4

The two CO-dehydrogenases of Thermococcus sp. AM4

Function and crystal structure of the dimeric P-loop ATPase CFD1 coordinating an exposed [4Fe-4S] cluster for transfer to apoproteins

Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase

Contact Info

Product

Resources

About