4OMF: The F420-reducing [NiFe]-hydrogenase complex from Methanothermobacter marburgensis, the first X-ray structure of a group 3 family member

Citation:
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 1.7A 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 degrees ' approximately -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.
PDB ID: 4OMFDownload
MMDB ID: 120639
PDB Deposition Date: 2014/1/27
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 1.71  Å
Source Organism:
Similar Structures:
Biological Unit for 4OMF: hexameric; determined by author and by software (PISA)
Molecular Components in 4OMF
Label Count Molecule
Proteins (6 molecules)
2
F420-reducing Hydrogenase, Subunit Gamma
Molecule annotation
2
F420-reducing Hydrogenase, Subunit Alpha
Molecule annotation
2
F420-reducing Hydrogenase, Subunit Beta
Molecule annotation
Chemicals (28 molecules)
1
8
2
2
3
2
4
6
5
2
6
2
7
2
8
2
9
2
* Click molecule labels to explore molecular sequence information.

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