9FSL | pdb_00009fsl

Crystal structure of CyuA from Methanococcus maripaludis with [2Fe-2S] clusters solved by Fe-SAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Evolution, structure and function of L-cysteine desulfidase, an enzyme involved in sulfur metabolism in the methanogenic archeon Methanococcus maripaludis.

Gervason, S.Zecchin, P.Shelton, E.B.He, N.Pecqueur, L.Garcia, P.S.Akinyemi, T.Touati, N.Bimai, O.Velours, C.Ravanat, J.L.Faivre, B.Whitman, W.B.Fontecave, M.Golinelli-Pimpaneau, B.

(2025) Commun Biol 8: 1667-1667

  • DOI: https://doi.org/10.1038/s42003-025-09053-0
  • Primary Citation of Related Structures:  
    9FSL

  • PubMed Abstract: 

    The biosynthesis of sulfur-containing molecules, which play essential roles in cell metabolism, often relies on enzymes that mobilize sulfur from cysteine. The function of such enzyme, L-cysteine desulfidase CyuA, which catalyzes L-cysteine decomposition to pyruvate, ammonia, and hydrogen sulfide, remains incompletely understood. Here, we used phylogenetic, genetic, biochemical, spectroscopic, and structural approaches to connect molecular structure to cellular physiology and evolutionary history and elucidate CyuA's role in sulfur metabolism. We found that Methanococcales and several other archaeal lineages acquired CyuA via horizontal gene transfer from bacteria. In Methanococcus maripaludis, CyuA (MmCyuA) stimulates growth in sulfide-rich conditions and enables slow growth with cysteine as the sole sulfur source. Crystallographic and biochemical data reveal that MmCyuA binds a [4Fe-4S] cluster coordinated by three conserved cysteines; the fourth ligand is a nonconserved cysteine in the wild-type enzyme but is replaced by glycerol or ethylene glycol in a variant. These results enabled modeling of the enzyme-substrate complex, allowing us to propose a detailed mechanism for L-cysteine desulfuration by CyuA, potentially involving a transient [4Fe-5S] species to transfer sulfur from cysteine to various [4Fe-4S]-dependent tRNA sulfuration enzymes. These findings advance understanding of sulfur activation and trafficking related to biosynthetic pathways leading to sulfur-containing compounds.


  • Organizational Affiliation
    • Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-cysteine desulfidase
A, B
400Methanococcus maripaludis S2Mutation(s): 0 
Gene Names: MMP1468
EC: 4.4.1.28
UniProt
Find proteins for Q6LX84 (Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL))
Explore Q6LX84 
Go to UniProtKB:  Q6LX84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LX84
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.166α = 90
b = 77.226β = 90
c = 153.969γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
BUSTERrefinement
PHASERphasing
PARROTphasing
CRANK2phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-11-LABX-0011

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references