Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.61 kDa 
• Atom Count: 6006 
• Residue Count: 789 
• Unique protein chains: 2

1PN3

Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and the acceptor substrate DVV.

• DOI: 10.2210/pdb1PN3/pdb

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


• Deposited: 2003-06-12 Released: 2003-08-12 
• Deposition Author(s): Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Structure of the Tdp-Epi-Vancosaminyltransferase Gtfa from the Chloroeremomycin Biosynthetic Pathway.

Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T., Garavito, R.M.

(2003) Proc Natl Acad Sci U S A 100: 9238

• PubMed: 12874381 
• DOI: 10.1073/pnas.1233577100
• Primary Citation of Related Structures:  
  1PN3, 1PNV


• PubMed Abstract: 
  

During the biosynthesis of the vancomycin-class antibiotic chloroeremomycin, TDP-epi-vancosaminyltransferase GtfA catalyzes the attachment of 4-epi-vancosamine from a TDP donor to the beta-OHTyr-6 of the aglycone cosubstrate. Glycosyltransferases from this pathway are potential tools for the combinatorial design of new antibiotics that are effective against vancomycin-resistant bacterial strains. These enzymes are members of the GT-B glycosyltransferase superfamily, which share a homologous bidomain topology. We present the 2.8-A crystal structures of GtfA complexes with vancomycin and the natural monoglycosylated peptide substrate, representing the first direct observation of acceptor substrate binding among closely related glycosyltransferases. The acceptor substrates bind to the N-terminal domain such that the aglycone substrate's reactive hydroxyl group hydrogen bonds to the side chains of Ser-10 and Asp-13, thus identifying these as residues of potential catalytic importance. As well as an open form of the enzyme, the crystal structures have revealed a closed form in which a TDP ligand is bound at a donor substrate site in the interdomain cleft, thereby illustrating not only binding interactions, but the conformational changes in the enzyme that accompany substrate binding.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSYLTRANSFERASE GTFA	A, B	404	Amycolatopsis orientalis	Mutation(s): 0  Gene Names: gtfA EC: 2.4.1.311
Find proteins for P96558 (Amycolatopsis orientalis) Explore P96558  Go to UniProtKB:  P96558

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DESVANCOSAMINYL VANCOMYCIN	C, D	7	Amycolatopsis orientalis	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYD	A	THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N
BGC	C, D	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OMY	C,D	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000205	C, D	DESVANCOSAMINYL VANCOMYCIN	Glycopeptide /  Antibiotic		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.249 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.5	α = 90
b = 152.5	β = 90
c = 98.74	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
RESOLVE	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-12 
• Released Date: 2003-08-12 
Deposition Author(s): Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T., Garavito, R.M.

Revision History 

• Version 1.0: 2003-08-12
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other
• Version 1.5: 2017-11-01
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Polymer sequence, Structure summary