Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.127 

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Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis.

Kobylarz, M.J.Grigg, J.C.Liu, Y.Lee, M.S.Heinrichs, D.E.Murphy, M.E.

(2016) Biochemistry 55: 927-939

  • DOI: https://doi.org/10.1021/acs.biochem.5b01045
  • Primary Citation of Related Structures:  
    5D84, 5D85, 5D86, 5D87

  • PubMed Abstract: 

    Staphylococcus aureus assembles the siderophore, staphyloferrin B, from l-2,3-diaminopropionic acid (l-Dap), α-ketoglutarate, and citrate. Recently, SbnA and SbnB were shown to produce l-Dap and α-ketoglutarate from O-phospho-l-serine (OPS) and l-glutamate. SbnA is a pyridoxal 5'-phosphate (PLP)-dependent enzyme with homology to O-acetyl-l-serine sulfhydrylases; however, SbnA utilizes OPS instead of O-acetyl-l-serine (OAS), and l-glutamate serves as a nitrogen donor instead of a sulfide. In this work, we examined how SbnA dictates substrate specificity for OPS and l-glutamate using a combination of X-ray crystallography, enzyme kinetics, and site-directed mutagenesis. Analysis of SbnA crystals incubated with OPS revealed the structure of the PLP-α-aminoacrylate intermediate. Formation of the intermediate induced closure of the active site pocket by narrowing the channel leading to the active site and forming a second substrate binding pocket that likely binds l-glutamate. Three active site residues were identified: Arg132, Tyr152, Ser185 that were essential for OPS recognition and turnover. The Y152F/S185G SbnA double mutant was completely inactive, and its crystal structure revealed that the mutations induced a closed form of the enzyme in the absence of the α-aminoacrylate intermediate. Lastly, l-cysteine was shown to be a competitive inhibitor of SbnA by forming a nonproductive external aldimine with the PLP cofactor. These results suggest a regulatory link between siderophore and l-cysteine biosynthesis, revealing a potential mechanism to reduce iron uptake under oxidative stress.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z3.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable siderophore biosynthesis protein SbnA326Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
Gene Names: sbnANWMN_0060
Find proteins for A6QDA0 (Staphylococcus aureus (strain Newman))
Explore A6QDA0 
Go to UniProtKB:  A6QDA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6QDA0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.08α = 90
b = 115.828β = 90
c = 45.138γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-102596

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence, Database references, Derived calculations