8TGS | pdb_00008tgs

The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with product UDP-Glucose and by-product analog VO4 (orthovanadate)

• PDB DOI: https://doi.org/10.2210/pdb8TGS/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-13 Released: 2025-01-22 
• Deposition Author(s): Prakash, O., Fuehring, J.I., Baruch, P., Routier, F.H., Fedorov, R.
• Funding Organization(s): German Research Foundation (DFG), European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

The post-reactive state structures of Leishmania major UDP-sugar pyrophosphorylase provide insights into the product release mechanism

Prakash, O., Fuehring, J.I., Baruch, P., Routier, F.H., Fedorov, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.64 kDa 
• Atom Count: 4,992 
• Modeled Residue Count: 608 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UTP-monosaccharide-1-phosphate uridylyltransferase	A	608	Leishmania major	Mutation(s): 0  Gene Names: USP EC: 2.7.7.64
UniProt
Find proteins for D3G6S4 (Leishmania major) Explore D3G6S4  Go to UniProtKB:  D3G6S4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
VO4 (Subject of Investigation/LOI)	C [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.08	α = 90
b = 122.42	β = 105.55
c = 61.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Prakash, O., Fuehring, J.I., Baruch, P., Routier, F.H., Fedorov, R.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FE 1510/2-1
European Union (EU)	European Union	EU FP7, GA. 608295

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release