5KEF

Structure of hypothetical Staphylococcus protein SA0856 with zinc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1080/07391102.2016.1278038
  • Structures With Same Primary Citation

  • 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 s ...

    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

    i X-CHIP Technologies Inc. , Toronto , Ontario , Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PhnB protein
A, B
153Staphylococcus aureus subsp. aureus CN1Mutation(s): 0 
Gene Names: SAKOR_02586
Find proteins for T1YBT4 (Staphylococcus aureus subsp. aureus CN1)
Go to UniProtKB:  T1YBT4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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