Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A5B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 232.86 kDa 
• Atom Count: 11483 
• Modelled Residue Count: 1412 
• Deposited Residue Count: 2016 
• Unique protein chains: 1

4M55

Crystal structure of Human UDP-xylose synthase R236H substitution

• PDB DOI: 10.2210/pdb4M55/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-08-08 Released: 2013-08-28 
• Deposition Author(s): Walsh Jr., R.M., Polizzi, S.J., Wood, Z.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.285 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Literature

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

• PubMed: 25521717 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucuronic acid decarboxylase 1	A, B, C, D, E, F	336	Homo sapiens	Mutation(s): 1  Gene Names: UNQ2538/PRO6079, UXS, UXS1 EC: 4.1.1.35
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBZ7 (Homo sapiens) Explore Q8NBZ7  Go to UniProtKB:  Q8NBZ7
PHAROS:  Q8NBZ7 GTEx:  ENSG00000115652

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth A], J [auth B], M [auth C], P [auth D], R [auth E], S [auth F]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UDP	K [auth B], Q [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
POP	H [auth A], N [auth C]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
SO4	I [auth A], L [auth B], O [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 0.285 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.171	α = 90
b = 85.145	β = 90
c = 292.549	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-08 
• Released Date: 2013-08-28 
Deposition Author(s): Walsh Jr., R.M., Polizzi, S.J., Wood, Z.A.

Revision History  

• Version 1.0: 2013-08-28
  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