5ODC

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus at 2.3 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.

Wagner, T.Koch, J.Ermler, U.Shima, S.

(2017) Science 357: 699-703

  • DOI: 10.1126/science.aan0425
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In methanogenic archaea, the carbon dioxide (CO <sub>2 </sub>) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferr ...

    In methanogenic archaea, the carbon dioxide (CO 2 ) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs. Soaking experiments showed that the heterodisulfide is clamped between the two noncubane [4Fe-4S] clusters and homolytically cleaved, forming coenzyme M and B bound to each iron. Coenzymes are consecutively released upon one-by-one electron transfer. The HdrABC-MvhAGD atomic model serves as a structural template for numerous HdrABC homologs involved in diverse microbial metabolic pathways.


    Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany.,Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany. shima@mpi-marburg.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heterodisulfide reductase, subunit A
A, G
654Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 1.8.98.1
Find proteins for A0A2D0TCB9 (Methanothermococcus thermolithotrophicus DSM 2095)
Go to UniProtKB:  A0A2D0TCB9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heterodisulfide reductase, subunit B
B, H
291Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 1.8.98.1
Find proteins for A0A2D0TCB4 (Methanothermococcus thermolithotrophicus DSM 2095)
Go to UniProtKB:  A0A2D0TCB4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Heterodisulfide reductase, subunit C
C, I
184Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 1.8.98.1
Find proteins for A0A2D0TC97 (Methanothermococcus thermolithotrophicus DSM 2095)
Go to UniProtKB:  A0A2D0TC97
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Methyl-viologen reducing hydrogenase subunit D
D, J
140Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 1.8.98.1
Find proteins for A0A2D0TC98 (Methanothermococcus thermolithotrophicus DSM 2095)
Go to UniProtKB:  A0A2D0TC98
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Methyl-viologen reducing hydrogenase subunit G
E, K
299Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 1.12.1.2, 1.12.99.6
Find proteins for A0A2D0TC99 (Methanothermococcus thermolithotrophicus DSM 2095)
Go to UniProtKB:  A0A2D0TC99
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Methyl-viologen reducing hydrogenase subunit A
F, L
473Methanothermococcus thermolithotrophicus DSM 2095Mutation(s): 0 
EC: 1.12.99.6, 1.12.1.2
Find proteins for A0A2D0TCA6 (Methanothermococcus thermolithotrophicus DSM 2095)
Go to UniProtKB:  A0A2D0TCA6
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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A, C, E, G, I, K
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
NA
Query on NA

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A, G
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B, F, G
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NFU
Query on NFU

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F, L
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
NI-FE REDUCED ACTIVE CENTER
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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A, G
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C, D, E, G, K
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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F, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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D, J
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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F, I
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
9S8
Query on 9S8

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B, H
Non-cubane [4Fe-4S]-cluster
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
 Ligand Interaction
PE3
Query on PE3

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A
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
POLYETHYLENE GLYCOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 378.047α = 90.00
b = 98.446β = 110.70
c = 137.884γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release