4TV5

Crystal Structure of Citrate Synthase SbnG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

SbnG, a Citrate Synthase in Staphylococcus aureus: A NEW FOLD ON AN OLD ENZYME.

Kobylarz, M.J.Grigg, J.C.Sheldon, J.R.Heinrichs, D.E.Murphy, M.E.

(2014) J Biol Chem 289: 33797-33807

  • DOI: 10.1074/jbc.M114.603175
  • Primary Citation of Related Structures:  
    4TV5, 4TV6

  • PubMed Abstract: 
  • In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway ...

    In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. We present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic gene clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. A structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production.


    Organizational Affiliation

    From the Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada and Michael.Murphy@ubc.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-dehydro-3-deoxyglucarate aldolaseA259Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
Gene Names: sbnGNWMN_0066
UniProt
Find proteins for A0A0H3K9Z0 (Staphylococcus aureus (strain Newman))
Explore A0A0H3K9Z0 
Go to UniProtKB:  A0A0H3K9Z0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3K9Z0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.29α = 90
b = 74.29β = 90
c = 76.72γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-29
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy