1TEX

Mycobacterium smegmatis Stf0 Sulfotransferase with Trehalose

• PDB DOI:  https://doi.org/10.2210/pdb1TEX/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-05-25 Released: 2004-07-20 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

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

• PubMed: 15258569 
• DOI: https://doi.org/10.1038/nsmb802
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stf0 Sulfotransferase	A, B, C, D	287	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: stf0, NCTC7017_01453 EC: 2.8.2
UniProt
Find proteins for P84151 (Mycolicibacterium smegmatis) Explore P84151  Go to UniProtKB:  P84151

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	E, F, G, H	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	E, F, G, H	trehalose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.274 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.929	α = 90
b = 101.929	β = 90
c = 228.212	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-20 
Deposition Author(s): 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.

Revision History  

• 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