4R7P

Human UDP-glucose pyrophosphorylase isoform 1 in complex with UDP-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Quaternary Mechanism Enables the Complex Biological Functions of Octameric Human UDP-glucose Pyrophosphorylase, a Key Enzyme in Cell Metabolism.

Fuhring, J.I.Cramer, J.T.Schneider, J.Baruch, P.Gerardy-Schahn, R.Fedorov, R.

(null) Sci Rep 5: 9618-9618

  • DOI: 10.1038/srep09618
  • Primary Citation of Related Structures:  
    4R7P

  • PubMed Abstract: 
  • In mammals, UDP-glucose pyrophosphorylase (UGP) is the only enzyme capable of activating glucose-1-phosphate (Glc-1-P) to UDP-glucose (UDP-Glc), a metabolite located at the intersection of virtually all metabolic pathways in the mammalian cell. Despite the essential role of its product, the molecular basis of UGP function is poorly understood ...

    In mammals, UDP-glucose pyrophosphorylase (UGP) is the only enzyme capable of activating glucose-1-phosphate (Glc-1-P) to UDP-glucose (UDP-Glc), a metabolite located at the intersection of virtually all metabolic pathways in the mammalian cell. Despite the essential role of its product, the molecular basis of UGP function is poorly understood. Here we report the crystal structure of human UGP in complex with its product UDP-Glc. Beyond providing first insight into the active site architecture, we describe the substrate binding mode and intermolecular interactions in the octameric enzyme that are crucial to its activity. Importantly, the quaternary mechanism identified for human UGP in this study may be common for oligomeric sugar-activating nucleotidyltransferases. Elucidating such mechanisms is essential for understanding nucleotide sugar metabolism and opens the perspective for the development of drugs that specifically inhibit simpler organized nucleotidyltransferases in pathogens.


    Organizational Affiliation

    1] Research Division for Structural Analysis, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany [2] Institute for Biophysical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UTP--glucose-1-phosphate uridylyltransferase ABCD526Homo sapiensMutation(s): 0 
Gene Names: UGP2UGP1
EC: 2.7.7.9
Find proteins for Q16851 (Homo sapiens)
Explore Q16851 
Go to UniProtKB:  Q16851
NIH Common Fund Data Resources
PHAROS:  Q16851
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UPG
Query on UPG

Download Ideal Coordinates CCD File 
A
URIDINE-5'-DIPHOSPHATE-GLUCOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.97α = 90
b = 138.97β = 90
c = 311.62γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
AMoREphasing
PHENIXrefinement
XDSdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release