9H7Y | pdb_00009h7y

SmsC2B2 complex from M. jannaschii (orthorhombic form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.290 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.272 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Ancestral [Fe-S] biogenesis system SMS has a unique mechanism of cluster assembly and sulfur utilization.

Dussouchaud, M.Martinez-Carranza, M.Garcia, P.S.Clemancey, M.Blondin, G.Betton, J.M.Haouz, A.Gribaldo, S.Ollagnier de Choudens, S.Sauguet, L.Mechaly, A.Barras, F.

(2025) PLoS Biol 23: e3003223-e3003223

  • DOI: https://doi.org/10.1371/journal.pbio.3003223
  • Primary Citation of Related Structures:  
    9H78, 9H7X, 9H7Y, 9HBL

  • PubMed Abstract: 

    [Fe-S] clusters are ancient and ubiquitous protein co-factors, which contributed to the emergence of life in an anoxic planet. We have recently identified two minimal [Fe-S] biogenesis systems, MIS and SMS, inferred to be ancestral systems dating back to the Last Universal Common Ancestor and which gave rise to the well-studied modern Iron-Sulfur Cluster (ISC), Nitrogen Fixation (NIF), and Sulfur Mobilization (SUF) machineries. The present study focuses on the ancestor SMS from the hyperthermophilic archaeon Methanocaldococcus jannaschii. Biochemical and structural studies showed that SMS is made of a SmsC2B2 heterotetratmer wherein the SmsC subunit hosts both ATP and [Fe-S] cluster binding sites. Binding of ATP and assembly of [Fe-S] were found to be mutually exclusive allowing for a regulatory coupling between binding of both substrates. Mutagenesis and in vitro transfer experiments revealed the key role of SmsC-contained Cys residues in cluster assembly. Strikingly, the SMS system rescued a non-viable Escherichia coli strain lacking endogenous ISC and SUF systems grown under anoxic conditions, in the presence of Na2S, indicating that sulfide is a source of sulfur for SMS. In addition, we predict that most archaea SmsC proteins hold a similar C-terminal [Fe-S] cluster assembly site. Taking into account those unique structural and functional features, we propose a mechanistic model describing how SmsC2B2 assembles and distributes [4Fe-4S] clusters. Altogether this study established SMS as a new bona fide [Fe-S] biogenesis system that operated in anaerobic prokaryotes prior to evolve to SUF after the Great Oxydation Event.


  • Organizational Affiliation
    • Department of Microbiology, Unit Stress Adaptation and Metabolism in Enterobacteria, Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Paris, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized ABC transporter ATP-binding protein MJ0035253Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0035
UniProt
Find proteins for Q60350 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q60350 
Go to UniProtKB:  Q60350
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60350
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-sulfur cluster assembly SufBD family protein MJ0034316Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0034
UniProt
Find proteins for Q60349 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q60349 
Go to UniProtKB:  Q60349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60349
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.290 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.272 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.167α = 90
b = 125.038β = 90
c = 133.056γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

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)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references