8RDH | pdb_00008rdh

Crystal structure of UDP-galactose 4-epimerase from Pyrococcus horikoshii with bound NAD and GDP-L-fucose

• PDB DOI: https://doi.org/10.2210/pdb8RDH/pdb

• Classification: ISOMERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-08 Released: 2024-12-18 
• Deposition Author(s): Thunnissen, A.M.W.H., Alvarez Quispe, C., Desmet, T.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: in silico

Literature

Structural, computational and biochemical analysis reveal new insights in the specificity of a promiscuous GDP-Gal4E

Alvarez Quispe, C., Savino, S., Biarnes, X., Planas, A., Thunnissen, A.M.W.H., Beerens, K., Desmet, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.93 kDa 
• Atom Count: 5,233 
• Modeled Residue Count: 634 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR family NAD(P)-dependent oxidoreductase	A, B	326	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: HA331_04725
UniProt
Find proteins for O73960 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O73960  Go to UniProtKB:  O73960

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GFB (Subject of Investigation/LOI)	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE C16 H25 N5 O15 P2 LQEBEXMHBLQMDB-JGQUBWHWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.331	α = 90
b = 97.262	β = 90
c = 117.252	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Thunnissen, A.M.W.H., Alvarez Quispe, C., Desmet, T.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1105922N
Research Foundation - Flanders (FWO)	Belgium	G0A7520N

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release