Crystal structure of YrbA from Sinorhizobium meliloti in complex with nickel.

Experimental Data Snapshot

  • Resolution: 0.98 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.102 

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Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines.

Roret, T.Alloing, G.Girardet, J.M.Perrot, T.Dhalleine, T.Couturier, J.Frendo, P.Didierjean, C.Rouhier, N.

(2020) Biosci Rep 40

  • DOI: https://doi.org/10.1042/BSR20202956
  • Primary Citation of Related Structures:  
    5NFK, 5NFL, 5NFM

  • PubMed Abstract: 

    Sinorhizobium meliloti is a nitrogen-fixing bacterium forming symbiotic nodules with the legume Medicago truncatula. S. meliloti possesses two BolA-like proteins (BolA and YrbA), the function of which is unknown. In organisms where BolA proteins and monothiol glutaredoxins (Grxs) are present, they contribute to the regulation of iron homeostasis by bridging a [2Fe-2S] cluster into heterodimers. A role in the maturation of iron-sulfur (Fe-S) proteins is also attributed to both proteins. In the present study, we have performed a structure-function analysis of SmYrbA showing that it coordinates diverse divalent metal ions (Fe2+, Co2+, Ni2+, Cu2+ and Zn2+) using His32 and His67 residues, that are also used for Fe-S cluster binding in BolA-Grx heterodimers. It also possesses the capacity to form heterodimers with the sole monothiol glutaredoxin (SmGrx2) present in this species. Using cellular approaches analyzing the metal tolerance of S. meliloti mutant strains inactivated in the yrbA and/or bolA genes, we provide evidence for a connection of YrbA with the regulation of iron homeostasis. The mild defects in M. truncatula nodulation reported for the yrbA bolA mutant as compared with the stronger defects in nodule development previously observed for a grx2 mutant suggest functions independent of SmGrx2. These results help in clarifying the physiological role of BolA-type proteins in bacteria.

  • Organizational Affiliation

    Université de Lorraine, INRAE, IAM, Nancy, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YrbA75Sinorhizobium meliloti 2011Mutation(s): 0 
Gene Names: SM2011_c00487
Find proteins for A0A452CS62 (Sinorhizobium meliloti (strain Sm2011 / Rm2011 / 2011))
Explore A0A452CS62 
Go to UniProtKB:  A0A452CS62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A452CS62
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 0.98 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.101 
  • R-Value Observed: 0.102 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.887α = 90
b = 31.917β = 90
c = 62.833γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references, Derived calculations, Structure summary