Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 64.12 kDa 
• Atom Count: 4219 
• Modelled Residue Count: 497 
• Deposited Residue Count: 562 
• Unique protein chains: 1

3CU0

human beta 1,3-glucuronyltransferase I (GlcAT-I) in complex with UDP and GAL-GAL(6-SO4)-XYL(2-PO4)-O-SER

• DOI: 10.2210/pdb3CU0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-15 Released: 2008-05-06 
• Deposition Author(s): Tone, Y., Pedersen, L.C., Yamamoto, T., Kitagawa, H., Nishihara-Shimizu, J., Tamura, J., Negishi, M., Sugahara, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

2-o-phosphorylation of xylose and 6-o-sulfation of galactose in the protein linkage region of glycosaminoglycans influence the glucuronyltransferase-I activity involved in the linkage region synthesis.

Tone, Y., Pedersen, L.C., Yamamoto, T., Izumikawa, T., Kitagawa, H., Nishihara, J., Tamura, J., Negishi, M., Sugahara, K.

(2008) J Biol Chem 283: 16801-16807

• PubMed: 18400750 
• DOI: 10.1074/jbc.M709556200
• Primary Citation of Related Structures:  
  3CU0


• PubMed Abstract: 
  

Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Glucuronyltransferase-I (GlcAT-I) is the key enzyme that completes the synthesis of this linkage region, which is a prerequisite for the conversion of core proteins to functional proteoglycans bearing GAGs. The Xyl and Gal residues in the linkage region can be modified by phosphorylation and sulfation, respectively, although the biological significance of these modifications remains to be clarified. Here we present evidence that these modifications can significantly influence the catalytic activity of GlcAT-I. Enzyme assays showed that the synthetic substrates, Gal-Gal-Xyl(2-O-phosphate)-O-Ser and Gal-Gal(6-O-sulfate)-Xyl(2-O-phosphate)-O-Ser, served as better substrates than the unmodified compound, whereas Gal(6-O-sulfate)-Gal-Xyl(2-O-phosphate)-O-Ser exhibited no acceptor activity. The crystal structure of the catalytic domain of GlcAT-I with UDP and Gal-Gal(6-O-sulfate)-Xyl(2-O-phosphate)-O-Ser bound revealed that the Xyl(2-O-phosphate)-O-Ser is disordered and the 6-O-sulfate forms interactions with Gln(318) from the second GlcAT-I monomer in the dimeric enzyme. The results indicate the possible involvement of these modifications in the processing and maturation of the growing linkage region oligosaccharide required for the assembly of GAG chains.

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Organizational Affiliation: 

Department of Biochemistry, Kobe Pharmaceutical University, Higashinada-ku, Kobe 658-8558, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3	A, B	281	Homo sapiens	Mutation(s): 0  Gene Names: B3GAT3 EC: 2.4.1.135
Find proteins for O94766 (Homo sapiens) Explore O94766  Go to UniProtKB:  O94766
NIH Common Fund Data Resources
PHAROS:  O94766 GTEx:  ENSG00000149541

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-3)-beta-D-galactopyranose	C, D	2		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	A	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.047	α = 90
b = 48.399	β = 92.4
c = 103.708	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
StructureStudio	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-15 
• Released Date: 2008-05-06 
Deposition Author(s): Tone, Y., Pedersen, L.C., Yamamoto, T., Kitagawa, H., Nishihara-Shimizu, J., Tamura, J., Negishi, M., Sugahara, K.

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary