1TEX | pdb_00001tex

Mycobacterium smegmatis Stf0 Sulfotransferase with Trehalose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.274 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis.

Mougous, J.D.Petzold, C.J.Senaratne, R.H.Lee, D.H.Akey, D.L.Lin, F.L.Munchel, S.E.Pratt, M.R.Riley, L.W.Leary, J.A.Berger, J.M.Bertozzi, C.R.

(2004) Nat Struct Mol Biol 11: 721-729

  • DOI: https://doi.org/10.1038/nsmb802
  • Primary Citation Related Structures: 
    1TEX

  • PubMed Abstract: 

    Sulfolipid-1 (SL-1) is an abundant sulfated glycolipid and potential virulence factor found in Mycobacterium tuberculosis. SL-1 consists of a trehalose-2-sulfate (T2S) disaccharide elaborated with four lipids. We identified and characterized a conserved mycobacterial sulfotransferase, Stf0, which generates the T2S moiety of SL-1. Biochemical studies demonstrated that the enzyme requires unmodified trehalose as substrate and is sensitive to small structural perturbations of the disaccharide. Disruption of stf0 in Mycobacterium smegmatis and M. tuberculosis resulted in the loss of T2S and SL-1 formation, respectively. The structure of Stf0 at a resolution of 2.6 A reveals the molecular basis of trehalose recognition and a unique dimer configuration that encloses the substrate into a bipartite active site. These data provide strong evidence that Stf0 carries out the first committed step in the biosynthesis of SL-1 and establish a system for probing the role of SL-1 in M. tuberculosis infection.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 131.36 kDa 
  • Atom Count: 7,919 
  • Modeled Residue Count: 973 
  • Deposited Residue Count: 1,148 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Stf0 Sulfotransferase
A, B, C, D
287Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: stf0
EC: 2.8.2
UniProt
Find proteins for P84151 (Mycolicibacterium smegmatis)
Explore P84151 
Go to UniProtKB:  P84151
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84151
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
E, F, G, H
2N/A
Glycosylation Resources
GlyTouCan: G92130SN
GlyCosmos: G92130SN

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.274 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.929α = 90
b = 101.929β = 90
c = 228.212γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-14
    Changes: Data collection, Database references, Structure summary