1IIR

Crystal Structure of UDP-glucosyltransferase GtfB

• PDB DOI: https://doi.org/10.2210/pdb1IIR/pdb

• Classification: TRANSFERASE
• Organism(s): Amycolatopsis orientalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-04-24 Released: 2001-07-18 
• Deposition Author(s): Mulichak, A.M., Losey, H.C., Walsh, C.T., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.211 

Literature

Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics.

Mulichak, A.M., Losey, H.C., Walsh, C.T., Garavito, R.M.

(2001) Structure 9: 547-557

• PubMed: 11470430 
• DOI: https://doi.org/10.1016/s0969-2126(01)00616-5
• Primary Citation of Related Structures:  
  1IIR


• PubMed Abstract: 
  

  Members of the vancomycin group of glycopeptide antibiotics have an oxidatively crosslinked heptapeptide scaffold decorated at the hydroxyl groups of 4-OH-Phegly4 or beta-OH-Tyr6 with mono- (residue 6) or disaccharides (residue 4). The disaccharide in vancomycin itself is L-vancosamine-1,2-glucose, and in chloroeremomycin it is L-4-epi-vancosamine-1,2-glucose. The sugars and their substituents play an important role in efficacy, particularly against vancomycin-resistant pathogenic enterococci.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.92 kDa 
• Atom Count: 3,092 
• Modelled Residue Count: 382 
• Deposited Residue Count: 415 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycosyltransferase GtfB	A	415	Amycolatopsis orientalis	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for P96559 (Amycolatopsis orientalis) Explore P96559  Go to UniProtKB:  P96559

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.231 
• R-Value Work: 0.211 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.11	α = 90
b = 102.11	β = 90
c = 83.35	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-18 
Deposition Author(s): Mulichak, A.M., Losey, H.C., Walsh, C.T., Garavito, R.M.

Revision History  

• Version 1.0: 2001-07-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations