8WXK | pdb_00008wxk

Crystal Structure of UDP-Glucose 4-Epimerase (all4713) with UDP-glucose and NAD from Nostoc sp. PCC 7120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Use of UDP-glucose 4-epimerase all4713 from Nostoc sp. PCC 7120 in the synthesis of galactose.

Huo, W.Sayed, H.Liu, M.Dai, G.Mayo, K.H.Su, J.

(2026) Arch Biochem Biophys 783: 110896-110896

  • DOI: https://doi.org/10.1016/j.abb.2026.110896
  • Primary Citation Related Structures: 
    8WXK

  • PubMed Abstract: 

    UDP-glucose 4-epimerase (GalE) is a key enzyme in the Leloir pathway that catalyzes the reversible conversion of UDP-glucose to UDP-galactose and plays a central role in galactose metabolism. To investigate the structural basis of this reaction in cyanobacteria, the protein encoded by all4713 from Nostoc sp. PCC 7120 was identified and characterized as a GalE enzyme. The protein was crystallized in complex with UDP-glucose and NAD + , and its structure revealed a typical epimerase fold consisting of nine α-helices and a seven-stranded β-sheet that together form the catalytic pocket accommodating both ligands. To probe the catalytic mechanism, seven active-site variants (A84K, T124A, T124S, A126T, A150K, H196 N, and L296 M) were generated by site-directed mutagenesis. Enzymatic assays indicated that the L296 M variant exhibited higher activity than the wild-type enzyme under the tested conditions, suggesting that this residue may influence substrate interactions within the catalytic site. Based on these findings, an enzymatic route for galactose generation was outlined in which sucrose synthase (SuSy) produces UDP-glucose from sucrose and UDP, followed by GalE-mediated conversion to UDP-galactose and subsequent hydrolysis to yield galactose. The resulting galactose can be further converted to tagatose by ʟ-arabinose isomerase. This work provides structural and functional insight into the GalE enzyme from Nostoc and supports its potential application in enzymatic sugar conversion processes.


  • Organizational Affiliation
    • Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun, 130024, China.

Macromolecule Content 

  • Total Structure Weight: 150.58 kDa 
  • Atom Count: 10,829 
  • Modeled Residue Count: 1,318 
  • Deposited Residue Count: 1,328 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-glucose 4-epimerase
A, B, C, D
332Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: all4713
EC: 5.1.3.2
UniProt
Find proteins for A0ACD6B995 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore A0ACD6B995 
Go to UniProtKB:  A0ACD6B995
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B995
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
UPG

Query on UPG



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
URIDINE-5'-DIPHOSPHATE-GLUCOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.229 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.16α = 90
b = 101.49β = 90
c = 167.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-10-30 
  • Deposition Author(s): Su, J.Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171255

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Database references