On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

Tan, Grace O.; Ensign, Scott A.; Ciurli, Stefano; Scott, Michael J.; Hedman, Britt; Holm, R. H.; Ludden, Paul W.; Korszun, Z. R.; Stephens, Philip J.

doi:10.1073/pnas.89.10.4427

Cited by 56 publications

(66 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…32,33 The intensity of the 1s→3d peak coupled with the shoulder at ~8338 eV is most consistent with a site that is a C 2v distortion of a square planar geometry, in agreement with the four ligands found in EXAFS analysis ( vide infra ). 33,34 The large 1s→3d peak area observed for Ni(II) H3E-RcnR is consistent with tetrahedral coordination. 32 However, the best fit of the EXAFS indicates the presence seven ligands ( vide infra) , and so tetrahedral geometry is not supported.…”

Section: Resultsmentioning

confidence: 72%

Role of the N-terminus in Determining Metal-Specific Responses in the E. coli Ni- and Co-Responsive Metalloregulator, RcnR

2012

View full text Add to dashboard Cite

RcnR (resistance to cobalt and nickel regulator) is a 40-kDa homotetrameric protein and metalloregulator that controls the transcription of the Co(II) and Ni(II) exporter, RcnAB, by binding to DNA as an apoprotein and releasing DNA in response to specifically binding Co(II) and Ni(II) ions. Using X-ray absorption spectroscopy (XAS) to examine the structure of metals bound and lacZ reporter assays of the transcription of RcnA in response to metal binding, in WT and mutant proteins, the roles of coordination number, ligand selection, and residues in the N-terminus of the protein were examined as determinants in metal ion recognition. The studies show that the cognate metal ions, Co(II) and Ni(II), which bind in (N/O) 5 S six-coordinate sites, are distinguished from non-cognate metal ions (Cu(I) and Zn(II)), which bind only three protein ligands and one anion from the buffer, by coordination number and ligand selection. Using mutations of residues near the N-terminus, the N-terminal amine is shown to be a ligand of the cognate metal ions that is missing in the complexes with non-cognate metal ions. The side chain of His3 is also shown to play an important role in distinguishing metal ions. The imidazole group is shown to be a ligand in the Co(II) RcnR complex, but not in the Zn(II) complex. Further, His3 does not appear to bind to Ni(II), providing a structural basis for the differential regulation of RcnAB by the two cognate ions. The Zn(II) complexes change coordination number in response to the residue in position three. In H3C-RcnR, the Zn(II) complex is fivecoordinate, and in H3E-RcnR the Zn(II) ion is bound to six protein ligands. The metric parameters of this unusual Zn(II) structure resemble those of the WT-Ni(II) complex, and the mutant protein is able to regulate expression of RcnAB in response to binding the non-cognate ion. The results are discussed within a protein allosteric model for gene regulation by metalloregulators.

show abstract

Section: Resultsmentioning

confidence: 72%

Role of the N-terminus in Determining Metal-Specific Responses in the E. coli Ni- and Co-Responsive Metalloregulator, RcnR

2012

View full text Add to dashboard Cite

show abstract

“…60 We are continuing our studies of MFe3Q4 clusters and their possible biological relevance. A forthcoming report will provide additional examples of reductive rearrangement reactions for the synthesis of these clusters.…”

Section: Structures (A) [Nife3q4(pp~3)(set)3]2- the Compoundsmentioning

confidence: 98%

Synthetic nickel-containing heterometal cubane-type clusters with NiFe3Q4 cores (Q = sulfur, selenium)

Ciurli¹,

Ross²,

Scott³

et al. 1992

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Reaction of the linear trinuclear Fe(II1) clusters [Fe3Q4(SEt), ), in acetonitrile solution affords the products [NiFe,Q4(PPh3)(SEt),l2-(Q = S (9), Se (10)) and [NiFe3Q4(SEt),13-(Q = S ( l l ) , Se (12)) in ca. 30% yield. The reactions involve reductive rearrangement of the initial cluster to a cuboidal fragment and capture of the nickel atom. The compounds (Et4N),[9/10] are isomorphous and contain cluster anions with the cubane-type [NiFe3Q4] I + core units and Ni-PPh3 and Fe-SEt terminal ligation. The compound (Et4N),[ 121 is isomorphous with (Et4N),[Fe4Se4(SEt),] and contains the same cubane unit but with all-thiolate terminal ligation and disordered Ni and Fe subsites. The dimensions of the [NiFe,Q,]'+ cores are closely similar to those of the more familiar [Fe4Q4]2+J+ cluster cores, rendering separation of the salts of the same cation and cluster charge difficult. Collective structural, magnetic, and spectroscopic results are consistent with the simplified charge distribution [Fe,Q4]I-(S = 5 / 2 ) + Ni2+ (S = 1) and an S = 3 / 2 ground state that arises from antiparallel coupling of the two fragment spins. This mode of spin coupling causes oppositely signed isotropic shifts of the identical ligands at Ni and Fe subsites. Subsite-differentiated cluster 9 undergoes regiospecific substitution reactions to afford products with phosphines, cyanide, and isonitrile at the Ni subsite. These reactions are often accompanied by formation of [Fe,S4(SEt),l2-s3-minority products. Comparison of properties of the synthetic clusters and of a reconstituted NiFe3S4 species formed with Pyrococcus furiosus ferredoxin (Conover, R. C.; Park, J.-B.; Adams, M. W.; Johnson, M. K. J. Am. Chem. Soc. 1990,112,4562) reveals that they are isoelectronic with the same ground state. Consequently, the protein-bound species almost certainly has the cubane-type structure of the synthetic cluster. Some seven types of heterometal cubane clusters MFe,S, (M = V, Nb, Mo, W, Re, Co, Ni) have now been prepared. Reductive rearrangement reactions are likely to provide routes to additional members of the set, several of which are good structural models for the immediate heterometal coordination environment in enzymes (M = V, Mo), but none of which has as yet been shown to occur naturally.

show abstract

“…Issues addressed include whether the Ni is part of the cubane (site M a , Scheme 1) or in a mononuclear site (site M b , Scheme 1). Extended x-ray absorption fine structure (EXAFS) spectroscopy comparing the R. rubrum CODH (EC 1.2.99.2) with model [NiFe 3 S 4 ] cubanes (10) and Mössbauer spectroscopy (7) favor a model for the C-cluster that contains one Ni atom in the M b site bridged to an Fe with usual coordination in the M a site (Ni-X-[Fe 4 S 4 ]). This unusual Fe is typically denoted as FCII.…”

mentioning

confidence: 99%

Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase

Drennan

Heo

Sintchak

et al. 2001

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

295

274

View full text Add to dashboard Cite

A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-Å 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 [NiFe3S4] and not [Fe4S4]. 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 [Fe4S4] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an ␣͞␤ (Rossmann-like) domain in the middle, and an ␣͞␤ (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe4S4] cluster and another [Fe4S4] 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. P hototrophic anaerobes such as Rhodospirillum rubrum have the ability to use CO as a sole carbon and energy source (1). This ability derives from the oxidation of CO to CO 2 catalyzed by carbon monoxide dehydrogenases (CODHs). Some CODH enzymes also participate in the synthesis or degradation of acetyl-CoA and are referred to as CODH͞acetyl CoA synthases (CODH͞ACS). The dual role of these CODH͞ACSs is found in CO 2 fixation to acetyl-CoA by acetogens via the well studied Wood͞Ljungdahl pathway (reviewed in ref.2). Methanogens also use CODH͞ACSs in the conversion of acetyl-CoA to methane. As a consequence of these activities, CODHs are essential for the proper regulation of environmental carbon monoxide. Each year, up to 10 8 tons of CO are oxidized to CO 2 by aerobic and anaerobic bacteria containing CODH enzymes (3). Prehistoric environments rich in CO and CO 2 and deficient in oxygen (4) prompt speculation that early life forms relied on CO͞CO 2 as prime sources of both carbon and energy. In an effort to understand the detailed biochemical workings of early and current life on CO, we present the three-dimensional structure of an anaerobic Ni-Fe-S CODH enzyme.CODHs catalyze the oxidation of carbon monoxide in the two-electron process.The mechanism of CO oxidation is thought to involve binding and deprotonation of an H 2 O molecule to form hydroxide at a unique Ni-Fe-S center called the C-cluster (5). CO is believed to bind to a site on the C-cluster adjacent to the hydroxide. Thus, a metal-bound hydroxide may attack the CO carbon. Then the resulting metal-COOH intermediate is deprotonated and CO 2 is lost to yield a two-electron-reduced C-cluster (reviewed in ref.2). In R. rubrum, electrons are pas...

show abstract

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

Cited by 56 publications

References 34 publications

Role of the N-terminus in Determining Metal-Specific Responses in the E. coli Ni- and Co-Responsive Metalloregulator, RcnR

Role of the N-terminus in Determining Metal-Specific Responses in the E. coli Ni- and Co-Responsive Metalloregulator, RcnR

Synthetic nickel-containing heterometal cubane-type clusters with NiFe3Q4 cores (Q = sulfur, selenium)

Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase

Contact Info

Product

Resources

About