9FMG | pdb_00009fmg

Methylthio-alkane reductase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Methylthio-alkane reductases use nitrogenase metalloclusters for carbon-sulfur bond cleavage.

Lago-Maciel, A.Soares, J.C.Zarzycki, J.Buchanan, C.J.Reif-Trauttmansdorff, T.Schmidt, F.V.Lometto, S.Paczia, N.Schuller, J.M.Hansen, D.F.Heller, G.T.Prinz, S.Hochberg, G.K.A.Pierik, A.J.Rebelein, J.G.

(2025) Nat Catal 8: 1086-1099

  • DOI: https://doi.org/10.1038/s41929-025-01426-2
  • Primary Citation Related Structures: 
    9FMG

  • PubMed Abstract: 

    Methylthio-alkane reductases convert methylated sulfur compounds to methanethiol and small hydrocarbons, a process with important environmental and biotechnological implications. These enzymes are classified as nitrogenase-like enzymes, despite lacking the ability to convert dinitrogen to ammonia, raising fundamental questions about the factors controlling their activity and specificity. Here we present the molecular structure of the methylthio-alkane reductase, which reveals large metalloclusters, including the P-cluster and the [Fe 8 S 9 C]-cluster, previously found only in nitrogenases. Our findings suggest that distinct metallocluster coordination, surroundings and substrate channels determine the activity of these related metalloenzymes. This study provides new insights into nitrogen fixation, sulfur-compound reduction and hydrocarbon production. We also shed light on the evolutionary history of P-cluster and [Fe 8 S 9 C]-cluster-containing reductases emerging before nitrogenases.


  • Organizational Affiliation
    • Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase519Rhodospirillum rubrumMutation(s): 0 
Gene Names: Rru_A0794
EC: 1.18.6.1 (PDB Primary Data), 1.18 (UniProt)
UniProt
Find proteins for Q2RW97 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RW97 
Go to UniProtKB:  Q2RW97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RW97
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase
B, C
466Rhodospirillum rubrumMutation(s): 0 
Gene Names: Rru_A0793
EC: 1.18.6.1 (PDB Primary Data), 1.18 (UniProt)
UniProt
Find proteins for Q2RW98 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RW98 
Go to UniProtKB:  Q2RW98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RW98
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase iron protein
D, E
297Rhodospirillum rubrumMutation(s): 0 
Gene Names: nifHRru_A0795
EC: 1.18.6.1 (PDB Primary Data), 1.18 (UniProt)
UniProt
Find proteins for Q2RW96 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
Explore Q2RW96 
Go to UniProtKB:  Q2RW96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RW96
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S5Q (Subject of Investigation/LOI)
Query on S5Q

Download Ideal Coordinates CCD File 
F [auth A]FeFe cofactor
C Fe8 S9
ARHQIUGQOSHZFD-UHFFFAOYSA-N
CLF (Subject of Investigation/LOI)
Query on CLF

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G [auth B]FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
H [auth D],
L [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
K [auth D]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
AF3
Query on AF3

Download Ideal Coordinates CCD File 
J [auth D],
N [auth E]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth D],
M [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTPHENIX1.21

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany446841743
Max Planck SocietyGermany--
Max Planck SocietyGermanyIMPRS - Principles of microbial life

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references