Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2BC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.73 kDa 
• Atom Count: 7815 
• Residue Count: 896 
• Unique protein chains: 3

4OMF

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

• DOI: 10.2210/pdb4OMF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermobacter marburgensis str. Marburg
• Mutation(s): No 


• Deposited: 2014-01-27 Released: 2014-06-11 
• Deposition Author(s): Vitt, S., Ma, K., Warkentin, E., Moll, J., Pierik, A., Shima, S., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.181 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 

Literature

The F420-Reducing [NiFe]-Hydrogenase Complex from Methanothermobacter marburgensis, the First X-ray Structure of a Group 3 Family Member.

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

(2014) J Mol Biol 426: 2813-2826

• PubMed: 24887099 
• DOI: 10.1016/j.jmb.2014.05.024
• Structures With Same Primary Citation


• PubMed 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.

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Organizational Affiliation: 

Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
F420-reducing hydrogenase, subunit gamma	G	275	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0  Gene Names: frhG, MTBMA_c16840 EC: 1.12.98.1
Find proteins for D9PYF7 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PYF7  Go to UniProtKB:  D9PYF7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
F420-reducing hydrogenase, subunit alpha	A	405	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0  Gene Names: frhA, MTBMA_c16860 EC: 1.12.98.1
Find proteins for D9PYF9 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PYF9  Go to UniProtKB:  D9PYF9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
F420-reducing hydrogenase, subunit beta	B	281	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0  Gene Names: frhB, MTBMA_c16830 EC: 1.12.98.1
Find proteins for D9PYF6 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore D9PYF6  Go to UniProtKB:  D9PYF6

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4	B, G	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
NFU	A	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C3 H Fe N2 Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N
DTZ	G	zinc(II)hydrogensulfide H2 S2 Zn KEQKAMYELZXRRN-UHFFFAOYSA-L
UNK	B	UNKNOWN C4 H9 N O2 QWCKQJZIFLGMSD-VKHMYHEASA-N
KEN	B	N,N-dimethylmethanamine C3 H9 N GETQZCLCWQTVFV-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	G	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.181 
• R-Value Work: 0.150 
• R-Value Observed: 0.152 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 233.16	α = 90
b = 233.16	β = 90
c = 233.16	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SADABS	data scaling
SHARP	phasing
SHELXD	phasing
Coot	model building
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-27 
• Released Date: 2014-06-11 
Deposition Author(s): Vitt, S., Ma, K., Warkentin, E., Moll, J., Pierik, A., Shima, S., Ermler, U.

Revision History 

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2018-06-20
  Changes: Data collection