PDBsum entry 4udy

Oxidoreductase

PDB id: 4udy

Contents

Protein chain

633 a.a.

Ligands

SF4

FES

WCC

0NM

Metals

FE2

Waters ×758

PDB id:

4udy

Name:

Oxidoreductase

Title:

Nco- bound to cluster c of ni,fe-co dehydrogenase at true-atomic resolution

Structure:

Carbon monoxide dehydrogenase 2. Chain: x. Synonym: codh 2, ni, fe-co dehydrogenase. Engineered: yes

Source:

Carboxydothermus hydrogenoformans. Organism_taxid: 129958. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.09Å R-factor: 0.136 R-free: 0.165

Authors:

J.Fesseler,J.-H.Jeoung,H.Dobbek

Key ref:

J.Fesseler et al. (2015). How the [NiFe4S4] Cluster of CO Dehydrogenase Activates CO2 and NCO(-). Angew Chem Int Ed Engl, 54, 8560-8564. PubMed id: 25926100 DOI: 10.1002/anie.201501778

Date:

12-Dec-14 Release date: 13-May-15

Protein chain

Q9F8A8  (COOS2_CARHZ) -  Carbon monoxide dehydrogenase 2 from Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)

Seq: 636 a.a.

Struc: 633 a.a.

Enzyme reactions

• Enzyme class: E.C.1.2.7.4 - anaerobic carbon-monoxide dehydrogenase.
• Reaction: CO + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O = 2 reduced [2Fe-2S]- [ferredoxin] + CO2 + 2 H⁺

CO (Bound ligand (Het Group name = 0NM) matches with 66.67% similarity) + 2 × oxidized [2Fe-2S]-[ferredoxin] + H2O = 2 × reduced [2Fe-2S]- [ferredoxin] + CO2 + 2 × H(+)

• Cofactor: Fe cation; Ni(2+); Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/anie.201501778

Angew Chem Int Ed Engl 54:8560-8564 (2015)

PubMed id: 25926100

How the [NiFe4S4] Cluster of CO Dehydrogenase Activates CO2 and NCO(-).

J.Fesseler, J.H.Jeoung, H.Dobbek.

ABSTRACT

Ni,Fe-containing CO dehydrogenases (CODHs) use a [NiFe4 S4 ] cluster, termed cluster C, to reversibly reduce CO2 to CO with high turnover number. Binding to Ni and Fe activates CO2 , but current crystal structures have insufficient resolution to analyze the geometry of bound CO2 and reveal the extent and nature of its activation. The crystal structures of CODH in complex with CO2 and the isoelectronic inhibitor NCO(-) are reported at true atomic resolution (dmin ≤1.1 Å). Like CO2 , NCO(-) is a μ2 ,η(2) ligand of the cluster and acts as a mechanism-based inhibitor. While bound CO2 has the geometry of a carboxylate group, NCO(-) is transformed into a carbamoyl group, thus indicating that both molecules undergo a formal two-electron reduction after binding and are stabilized by substantial π backbonding. The structures reveal the combination of stable μ2 ,η(2) coordination by Ni and Fe2 with reductive activation as the basis for both the turnover of CO2 and inhibition by NCO(-) .