PDBsum entry 3cf4

Oxidoreductase

PDB id: 3cf4

Contents

Protein chains

766 a.a.

169 a.a.

Ligands

SF4 ×4

WCC-CMO

ACY ×11

GOL ×3

PEG

Metals

_FE

Waters ×542

References listed in PDB file

Key reference

Title

Structure of the alpha2epsilon2 ni-Dependent co dehydrogenase component of the methanosarcina barkeri acetyl-Coa decarbonylase/synthase complex.

Authors

W.Gong, B.Hao, Z.Wei, D.J.Ferguson, T.Tallant, J.A.Krzycki, M.K.Chan.

Ref.

Proc Natl Acad Sci U S A, 2008, 105, 9558-9563. [DOI no: 10.1073/pnas.0800415105]

PubMed id

18621675

Abstract

Ni-dependent carbon monoxide dehydrogenases (Ni-CODHs) are a diverse family of enzymes that catalyze reversible CO:CO(2) oxidoreductase activity in acetogens, methanogens, and some CO-using bacteria. Crystallography of Ni-CODHs from CO-using bacteria and acetogens has revealed the overall fold of the Ni-CODH core and has suggested structures for the C cluster that mediates CO:CO(2) interconversion. Despite these advances, the mechanism of CO oxidation has remained elusive. Herein, we report the structure of a distinct class of Ni-CODH from methanogenic archaea: the alpha(2)epsilon(2) component from the alpha(8)beta(8)gamma(8)delta(8)epsilon(8) CODH/acetyl-CoA decarbonylase/synthase complex, an enzyme responsible for the majority of biogenic methane production on Earth. The structure of this Ni-CODH component provides support for a hitherto unobserved state in which both CO and H(2)O/OH(-) bind to the Ni and the exogenous FCII iron of the C cluster, respectively, and offers insight into the structures and functional roles of the epsilon-subunit and FeS domain not present in nonmethanogenic Ni-CODHs.

Figure 1.
The M. barkeri α[2]ε[2] Ni-CODH component, subunits, and cofactors. (A) Side view of the α[2]ε[2] component. The protein is shown as ribbons with the α-subunits colored in cyan and green and the ε-subunits in tan and orange. The atoms of the metal clusters are shown as spheres, with Fe atoms colored in purple, Ni atoms in blue, and the remaining atoms in CPK. (B) Side view of metal clusters in the α[2]ε[2] complex. (C) Top view of the α[2]ε[2] component. (D) Top view of the right α-subunit highlighting its different domains. The ε-subunit is omitted. The α-subunit is colored in rainbow by domain: N-terminal portion (magenta), N-terminal α-helical domain (blue), first Rossmann-like domain (cyan), FeS-binding domain (green), second C-cluster Rossmann-like domain (yellow), and C-terminal domain (orange). The β-hairpin insert in the second Rossmann-like domain is colored in red. (E) Ribbon diagram of ε-subunit colored by secondary structure with α-helices in tan, β-sheets in magenta, and loops in cyan. The orientation of this subunit matches the ε-subunit shown as tan surface in F. (F) Docking interaction between the α- and ε-subunits colored as in A. The left ε-subunit is shown as a surface with an FAD molecule shown and colored in CPK to illustrate its fit to the cavity. No FAD was observed in the α[2]ε[2] structure. The β-strands in the right ε-subunit are colored in marine for better visualization.

Figure 2.
Structure of the C cluster, putative substrate channels, and proposed mechanism of C-O bond formation. (A) Stick diagram of the C cluster and surrounding residues together with surface diagram highlighting internal cavities. The atoms of the C cluster including the bound CO and putative H[2]O are colored by atom with Fe in violet, Ni in slate, carbon in gray, and sulfur in CPK. The protein is shown in stick with the carbon atoms depicted in cyan and the remaining atoms in CPK. The Ni and FCII iron that bind CO and H[2]O/OH, respectively, are labeled as are residues Ile-641 and His-117, which may help CO adopt its bent geometry. (B) Stick diagram highlighting putative proton/water channel. The conserved His residues that line one side of this channel are labeled. (C) The CO/CO[2] channel of methanogenic CODH component depicted as a transparent molecular surface component colored by subunit according to the color scheme in Fig. 1. The protein atoms have been omitted for clarity, but the metal clusters are shown as spheres with Fe atoms colored in violet, Ni atoms in slate, and the remaining atoms in CPK. The Xe-binding sites that map the channel are shown as pink spheres. A small molecule modeled as a portion of a PEG group is shown in stick and colored in CPK. This PEG molecule marks the channel exit from the ε-subunit. (D) Proposed coupling of the CO and H[2]O species via intermediate observed in this structure. The loss of the proton required for CO + OH^− bond formation may account for the stability of the current intermediate, which was crystallized at low pH. All other Ni-CODH structures have been determined at neutral pH.