5UJE

SbnI with C-terminal truncation from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in Staphylococcus aureus .

Verstraete, M.M.Perez-Borrajero, C.Brown, K.L.Heinrichs, D.E.Murphy, M.E.P.

(2018) J Biol Chem 293: 6147-6160

  • DOI: https://doi.org/10.1074/jbc.RA118.001875
  • Primary Citation of Related Structures:  
    5UJE

  • PubMed Abstract: 

    Staphyloferrin B (SB) is an iron-chelating siderophore produced by Staphylococcus aureus in invasive infections. Proteins for SB biosynthesis and export are encoded by the sbnABCDEFGHI gene cluster, in which SbnI, a member of the ParB/Srx superfamily, acts as a heme-dependent transcriptional regulator of the sbn locus. However, no structural or functional information about SbnI is available. Here, a crystal structure of SbnI revealed striking structural similarity to an ADP-dependent free serine kinase, SerK, from the archaea Thermococcus kodakarensis We found that features of the active sites are conserved, and biochemical assays and 31 P NMR and HPLC analyses indicated that SbnI is also a free serine kinase but uses ATP rather than ADP as phosphate donor to generate the SB precursor O -phospho-l-serine (OPS). SbnI consists of two domains, and elevated B -factors in domain II were consistent with the open-close reaction mechanism previously reported for SerK. Mutagenesis of Glu 20 and Asp 58 in SbnI disclosed that they are required for kinase activity. The only known OPS source in bacteria is through the phosphoserine aminotransferase activity of SerC within the serine biosynthesis pathway, and we demonstrate that an S. aureus serC mutant is a serine auxotroph, consistent with a function in l-serine biosynthesis. However, the serC mutant strain could produce SB when provided l-serine, suggesting that SbnI produces OPS for SB biosynthesis in vivo These findings indicate that besides transcriptionally regulating the sbn locus, SbnI also has an enzymatic role in the SB biosynthetic pathway.


  • Organizational Affiliation

    From the Department of Microbiology and Immunology and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SbnI protein242Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
Gene Names: sbnINWMN_0068
UniProt
Find proteins for Q2G1M5 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G1M5 
Go to UniProtKB:  Q2G1M5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G1M5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.12α = 90
b = 55.12β = 90
c = 92.69γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-49597

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2020-12-30
    Changes: Database references