2OVF | pdb_00002ovf

Crystal Structure of StaL-PAP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.269 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Crystal structure of StaL, a glycopeptide antibiotic sulfotransferase from Streptomyces toyocaensis.

Shi, R.Lamb, S.S.Bhat, S.Sulea, T.Wright, G.D.Matte, A.Cygler, M.

(2007) J Biological Chem 282: 13073-13086

  • DOI: https://doi.org/10.1074/jbc.M611912200
  • Primary Citation Related Structures: 
    2OV8, 2OVB, 2OVF

  • PubMed Abstract: 

    Over the past decade, antimicrobial resistance has emerged as a major public health crisis. Glycopeptide antibiotics such as vancomycin and teicoplanin are clinically important for the treatment of Gram-positive bacterial infections. StaL is a 3'-phosphoadenosine 5'-phosphosulfate-dependent sulfotransferase capable of sulfating the cross-linked heptapeptide substrate both in vivo and in vitro, yielding the product A47934, a unique teicoplanin-class glycopeptide antibiotic. The sulfonation reaction catalyzed by StaL constitutes the final step in A47934 biosynthesis. Here we report the crystal structure of StaL and its complex with the cofactor product 3'-phosphoadenosine 5'-phosphate. This is only the second prokaryotic sulfotransferase to be structurally characterized. StaL belongs to the large sulfotransferase family and shows higher similarity to cytosolic sulfotransferases (ST) than to the bacterial ST (Stf0). StaL has a novel dimerization motif, different from any other STs that have been structurally characterized. We have also applied molecular modeling to investigate the binding mode of the unique substrate, desulfo-A47934. Based on the structural analysis and modeling results, a series of residues was mutated and kinetically characterized. In addition to the conserved residues (Lys(12), His(67), and Ser(98)), molecular modeling, fluorescence quenching experiments, and mutagenesis studies identified several other residues essential for substrate binding and/or activity, including Trp(34), His(43), Phe(77), Trp(132), and Glu(205).


  • Organizational Affiliation
    • Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6.

Macromolecule Content 

  • Total Structure Weight: 32.64 kDa 
  • Atom Count: 1,912 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
StaL288Streptomyces toyocaensisMutation(s): 0 
Gene Names: stal
EC: 2.8.2.36
UniProt
Find proteins for Q8KLM3 (Streptomyces toyocaensis)
Explore Q8KLM3 
Go to UniProtKB:  Q8KLM3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KLM3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P

Query on A3P



Download:Ideal Coordinates CCD File
B [auth A]ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.269 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.392α = 90
b = 87.392β = 90
c = 169.377γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary