PDBsum entry 4omf

Oxidoreductase

PDB id: 4omf

Contents

Protein chains

231 a.a.

385 a.a.

280 a.a.

Ligands

SF4 ×4

DTZ

UNL

NFU

KEN

UNL-FAD

Metals

_CL

_MG ×4

Waters ×761

PDB id:

4omf

Name:

Oxidoreductase

Title:

The f420-reducing [nife]-hydrogenase complex from methanothermobacter marburgensis, the first x-ray structure of a group 3 family member

Structure:

F420-reducing hydrogenase, subunit gamma. Chain: g. F420-reducing hydrogenase, subunit alpha. Chain: a. F420-reducing hydrogenase, subunit beta. Chain: b. Ec: 1.12.98.1

Source:

Methanothermobacter marburgensis. Organism_taxid: 79929. Strain: dsm 2133 / 14651 / nbrc 100331 / ocm 82 / marburg. Strain: dsm 2133 / 14651 / nbrc 100331 / ocm 82 / marburg

Resolution:

1.71Å R-factor: 0.152 R-free: 0.181

Authors:

S.Vitt,K.Ma,E.Warkentin,J.Moll,A.Pierik,S.Shima,U.Ermler

Key ref:

S.Vitt et al. (2014). The F₄₂₀-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member. J Mol Biol, 426, 2813-2826. PubMed id: 24887099 DOI: 10.1016/j.jmb.2014.05.024

Date:

27-Jan-14 Release date: 11-Jun-14

Protein chain

D9PYF7  (D9PYF7_METTM) -  Coenzyme F420 hydrogenase subunit gamma from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)

Seq: 275 a.a.

Struc: 231 a.a.

Protein chain

D9PYF9  (D9PYF9_METTM) -  Coenzyme F420 hydrogenase subunit alpha from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)

Seq: 405 a.a.

Struc: 385 a.a.

Protein chain

D9PYF6  (D9PYF6_METTM) -  Coenzyme F420 hydrogenase subunit beta from Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)

Seq: 281 a.a.

Struc: 280 a.a.

Enzyme reactions

• Enzyme class: Chains G, A, B: E.C.1.12.98.1 - coenzyme F420 hydrogenase.
• Pathway: Coenzyme F₄₂₀ hydrogenase
• Reaction: oxidized coenzyme F420-(gamma-L-Glu)(n) + H2 + H⁺ = reduced coenzyme F420-(gamma-L-Glu)(n)
• Cofactor: FAD; Fe cation; Ni(2+)

FAD (Bound ligand (Het Group name = FAD) corresponds exactly) Fe cation Ni(2+)

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

Added reference

DOI no: 10.1016/j.jmb.2014.05.024

J Mol Biol 426:2813-2826 (2014)

PubMed id: 24887099

The F₄₂₀-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member.

S.Vitt, K.Ma, E.Warkentin, J.Moll, A.J.Pierik, S.Shima, U.Ermler.

ABSTRACT

The reversible redox reaction between coenzyme F420 and H2 to F420H2 is catalyzed by an F420-reducing [NiFe]-hydrogenase (FrhABG), which is an enzyme of the energy metabolism of methanogenic archaea. FrhABG is a group 3 [NiFe]-hydrogenase with a dodecameric quaternary structure of 1.25MDa as recently revealed by high-resolution cryo-electron microscopy. We report on the crystal structure of FrhABG from Methanothermobacter marburgensis at 1.7Å resolution and compare it with the structures of group 1 [NiFe]-hydrogenases, the only group structurally characterized yet. FrhA is similar to the large subunit of group 1 [NiFe]-hydrogenases regarding its core structure and the embedded [NiFe]-center but is different because of the truncation of ca 160 residues that results in similar but modified H2 and proton transport pathways and in suitable interfaces for oligomerization. The small subunit FrhG is composed of an N-terminal domain related to group 1 enzymes and a new C-terminal ferredoxin-like domain carrying the distal and medial [4Fe-4S] clusters. FrhB adopts a novel fold, binds one [4Fe-4S] cluster as well as one FAD in a U-shaped conformation and provides the F420-binding site at the Si-face of the isoalloxazine ring. Similar electrochemical potentials of both catalytic reactions and the electron-transferring [4Fe-4S] clusters, determined to be E°'≈-400mV, are in full agreement with the equalized forward and backward rates of the FrhABG reaction. The protein might contribute to balanced redox potentials by the aspartate coordination of the proximal [4Fe-4S] cluster, the new ferredoxin module and a rather negatively charged FAD surrounding.