8YP3 | pdb_00008yp3

Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase from Spodoptera frugiperda in complex with UDP-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.220 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.192 (Depositor) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure and Inhibition of Insect UDP- N -acetylglucosamine Pyrophosphorylase: A Key Enzyme in the Hexosamine Biosynthesis Pathway.

Lu, Q.Zhou, Y.Ding, Y.Cui, Y.Li, W.Liu, T.

(2024) J Agric Food Chem 72: 19286-19294

  • DOI: https://doi.org/10.1021/acs.jafc.4c03834
  • Primary Citation Related Structures: 
    8YP3

  • PubMed Abstract: 

    UDP- N -acetylglucosamine pyrophosphorylase (UAP) catalyzes the last step in the hexosamine biosynthesis pathway to directly produce UDP- N -acetylglucosamine (UDP-GlcNAc). Because UAPs play important physiological and pathological roles in organisms, they are considered potential targets for drug and pesticide development. However, the lack of efficient and selective inhibitors is a bottleneck that must be overcome. This study reports the first crystal structure of the insect UAP from Spodoptera frugiperda ( Sf UAP) in complex with UDP-GlcNAc. Sf UAP has two insect-specific structural characteristics in the active pocket, namely, a free Cys (Cys 334 ) and a Mg 2+ binding site, which differentiate it from human UAP ( Hs AGX1) and fungal UAP ( Af UAP) in terms of substrate and inhibitor binding. N -(4-Nitrophenyl)maleimide ( p NPMI) and myricetin are discovered as potent covalent and noncovalent inhibitors of Sf UAP, respectively. Moreover, myricetin can significantly reduce the level of cellular O -GlcNAcylation by inhibiting both UAP and O -GlcNAc transferase. These findings provide novel insights into the development of UAP-based drugs and pesticides.


  • Organizational Affiliation
    • MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China.

Macromolecule Content 

  • Total Structure Weight: 220.83 kDa 
  • Atom Count: 15,945 
  • Modeled Residue Count: 1,858 
  • Deposited Residue Count: 1,928 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine diphosphorylase
A, B, C, D
482Spodoptera frugiperdaMutation(s): 0 
Gene Names: SFRICE_001055
EC: 2.7.7.23
UniProt
Find proteins for A0A2H1VI03 (Spodoptera frugiperda)
Explore A0A2H1VI03 
Go to UniProtKB:  A0A2H1VI03
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H1VI03
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UD1
(Subject of Investigation/LOI)

Query on UD1



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C],
N [auth D]
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-CFRASDGPSA-N
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C],
O [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
M [auth C],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.220 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.192 (Depositor) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.734α = 90
b = 233.527β = 90.113
c = 98.063γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Database references