Crystal structure of Human UDP-xylose synthase R236A substitution

Experimental Data Snapshot

  • Resolution: 2.64 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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This is version 1.4 of the entry. See complete history


Man o' war mutation in UDP-alpha-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation.

Walsh Jr., R.M.Polizzi, S.J.Kadirvelraj, R.Howard, W.W.Wood, Z.A.

(2015) Biochemistry 54: 807-819

  • DOI: https://doi.org/10.1021/bi501357c
  • Primary Citation of Related Structures:  
    4LK3, 4M55

  • PubMed Abstract: 

    The man o' war (mow) phenotype in zebrafish is characterized by severe craniofacial defects due to a missense mutation in UDP-α-d-xylose synthase (UXS), an essential enzyme in proteoglycan biosynthesis. The mow mutation is located in the UXS dimer interface ∼16 Å away from the active site, suggesting an indirect effect on the enzyme mechanism. We have examined the structural and catalytic consequences of the mow mutation (R236H) in the soluble fragment of human UXS (hUXS), which shares 93% sequence identity with the zebrafish enzyme. In solution, hUXS dimers undergo a concentration-dependent association to form a tetramer. Sedimentation velocity studies show that the R236H substitution induces the formation of a new hexameric species. Using two new crystal structures of the hexamer, we show that R236H and R236A substitutions cause a local unfolding of the active site that allows for a rotation of the dimer interface necessary to form the hexamer. The disordered active sites in the R236H and R236A mutant constructs displace Y231, the essential acid/base catalyst in the UXS reaction mechanism. The loss of Y231 favors an abortive catalytic cycle in which the reaction intermediate, UDP-α-d-4-keto-xylose, is not reduced to the final product, UDP-α-d-xylose. Surprisingly, the mow-induced hexamer is almost identical to the hexamers formed by the deeply divergent UXS homologues from Staphylococcus aureus and Helicobacter pylori (21% and 16% sequence identity, respectively). The persistence of a latent hexamer-building interface in the human enzyme suggests that the ancestral UXS may have been a hexamer.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glucuronic acid decarboxylase 1
A, B, C, D, E
A, B, C, D, E, F
336Homo sapiensMutation(s): 1 
Gene Names: UNQ2538/PRO6079UXSUXS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBZ7 (Homo sapiens)
Explore Q8NBZ7 
Go to UniProtKB:  Q8NBZ7
GTEx:  ENSG00000115652 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBZ7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
DA [auth F]
G [auth A]
L [auth B]
Q [auth C]
U [auth D]
DA [auth F],
G [auth A],
L [auth B],
Q [auth C],
U [auth D],
Z [auth E]
C21 H27 N7 O14 P2
Query on UGA

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BA [auth E]
EA [auth F]
I [auth A]
N [auth B]
R [auth C]
BA [auth E],
EA [auth F],
I [auth A],
N [auth B],
R [auth C],
W [auth D]
C15 H22 N2 O18 P2
Query on UDP

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H [auth A],
M [auth B],
V [auth D]
C9 H14 N2 O12 P2
Query on POP

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AA [auth E],
FA [auth F],
S [auth C]
H2 O7 P2
Query on SO4

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CA [auth E]
GA [auth F]
J [auth A]
K [auth A]
O [auth B]
CA [auth E],
GA [auth F],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
T [auth C],
X [auth D],
Y [auth D]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.64 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.57α = 90
b = 92.07β = 90
c = 290.95γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description