4ECM

2.3 Angstrom Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Bacillus anthracis in Complex with Thymidine-5-diphospho-alpha-D-glucose and Pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA).

Baumgartner, J.Lee, J.Halavaty, A.S.Minasov, G.Anderson, W.F.Kuhn, M.L.

(2017) Acta Crystallogr F Struct Biol Commun 73: 621-628

  • DOI: 10.1107/S2053230X17015357

  • PubMed Abstract: 
  • L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structu ...

    L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structure of the first protein of this pathway, glucose-1-phosphate thymidylyltransferase (RfbA), from Bacillus anthracis was determined. In other organisms this enzyme is referred to as RmlA. RfbA was co-crystallized with the products of the enzymatic reaction, dTDP-α-D-glucose and pyrophosphate, and its structure was determined at 2.3 Å resolution. This is the first reported thymidylyltransferase structure from a Gram-positive bacterium. RfbA shares overall structural characteristics with known RmlA homologs. However, RfbA exhibits a shorter sequence at its C-terminus, which results in the absence of three α-helices involved in allosteric site formation. Consequently, RfbA was observed to exhibit a quaternary structure that is unique among currently reported glucose-1-phosphate thymidylyltransferase bacterial homologs. These structural analyses suggest that RfbA may not be allosterically regulated in some organisms and is structurally distinct from other RmlA homologs.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, San Francisco State University, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucose-1-phosphate thymidylyltransferase
A
269Bacillus anthracisMutation(s): 0 
Find proteins for A0A1Q4M367 (Bacillus anthracis)
Go to UniProtKB:  A0A1Q4M367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
DAU
Query on DAU

Download SDF File 
Download CCD File 
A
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
C16 H26 N2 O16 P2
YSYKRGRSMLTJNL-URARBOGNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 135.072α = 90.00
b = 135.072β = 90.00
c = 85.138γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement
Blu-Icedata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-05-23
    Type: Atomic model
  • Version 1.2: 2017-11-15
    Type: Database references, Refinement description