4OMF

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

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 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


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

  • DOI: 10.1016/j.jmb.2014.05.024
  • Primary Citation of Related Structures:  
    4OMF

  • 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 ...

    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.

    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: ulrich.ermler@biophys.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F420-reducing hydrogenase, subunit gammaA [auth G]275Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: frhG, MTBMA_c16840
EC: 1.12.98.1
UniProt
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9PYF7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
F420-reducing hydrogenase, subunit alphaB [auth A]405Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: frhA, MTBMA_c16860
EC: 1.12.98.1
UniProt
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9PYF9
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
F420-reducing hydrogenase, subunit betaC [auth B]281Methanothermobacter marburgensis str. MarburgMutation(s): 0 
Gene Names: frhB, MTBMA_c16830
EC: 1.12.98.1
UniProt
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9PYF6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
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R [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
SF4
Query on SF4
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D [auth G],
E [auth G],
F [auth G],
N [auth B]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
NFU
Query on NFU
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J [auth A]formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N		 Ligand Interaction
DTZ
Query on DTZ
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G zinc(II)hydrogensulfide
H2 S2 Zn
KEQKAMYELZXRRN-UHFFFAOYSA-L		 Ligand Interaction
UNK
Query on UNK
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Q [auth B]UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N		 Ligand Interaction
KEN
Query on KEN
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P [auth B]N,N-dimethylmethanamine
C3 H9 N
GETQZCLCWQTVFV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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M [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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I [auth A],
K [auth A],
L [auth A],
O [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
Download Ideal Coordinates CCD File 
H [auth G]Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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 = 233.16α = 90
b = 233.16β = 90
c = 233.16γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SADABSdata scaling
SHARPphasing
SHELXDphasing
Cootmodel building
PHENIXrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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