Structure of hypothetical Staphylococcus protein SA0856 with zinc

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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Crystal structure of Staphylococcus aureus Zn-glyoxalase I: new subfamily of glyoxalase I family.

Chirgadze, Y.N.Boshkova, E.A.Battaile, K.P.Mendes, V.G.Lam, R.Chan, T.S.Y.Romanov, V.Pai, E.F.Chirgadze, N.Y.

(2018) J Biomol Struct Dyn 36: 376-386

  • DOI: https://doi.org/10.1080/07391102.2016.1278038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structures of protein SA0856 from Staphylococcus aureus in its apo-form and in complex with a Zn 2+ -ion have been presented. The 152 amino acid protein consists of two similar domains with α + β topology. In both crystalline state and in solution, the protein forms a dimer with monomers related by a twofold pseudo-symmetry rotation axis. A sequence homology search identified the protein as a member of the structural family Glyoxalase I. We have shown that the enzyme possesses glyoxalase I activity in the presence of Zn 2+ , Mg 2+ , Ni 2+ , and Co 2+ , in this order of preference. Sequence and structure comparisons revealed that human glyoxalase I should be assigned to a subfamily A, while S. aureus glyoxalase I represents a new subfamily B, which includes also proteins from other bacteria. Both subfamilies have a similar protein chain fold but rather diverse sequences. The active sites of human and staphylococcus glyoxalases I are also different: the former contains one Zn-ion per chain; the latter incorporates two of these ions. In the active site of SA0856, the first Zn-ion is well coordinated by His58, Glu60 from basic molecule and Glu40*, His44* from adjacent symmetry-related molecule. The second Zn3-ion is coordinated only by residue His143 from protein molecule and one acetate ion. We suggest that only single Zn1-ion plays the role of catalytic center. The newly found differences between the two subfamilies could guide the design of new drugs against S. aureus, an important pathogenic micro-organism.

  • Organizational Affiliation

    c Department of Biochemistry , University of Cambridge , Cambridge CB2 1GA , UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PhnB protein
A, B
153Staphylococcus aureus subsp. aureus CN1Mutation(s): 0 
Gene Names: SAKOR_02586
Find proteins for T1YBT4 (Staphylococcus aureus subsp. aureus CN1)
Explore T1YBT4 
Go to UniProtKB:  T1YBT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1YBT4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.867α = 90
b = 92.611β = 90
c = 95.259γ = 90
Software Package:
Software NamePurpose
AutoPROCdata scaling
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ontario Research and Development Challenge FundCanada99-SEP-0512

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references