1KWS | pdb_00001kws

CRYSTAL STRUCTURE OF BETA1,3-GLUCURONYLTRANSFERASE I IN COMPLEX WITH THE ACTIVE UDP-GLCUA DONOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.223 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1KWS

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA.

Pedersen, L.C., Darden, T.A., Negishi, M.

(2002) J Biological Chem 277: 21869-21873

  • DOI: https://doi.org/10.1074/jbc.M112343200
  • Primary Citation Related Structures: 
    1KWS

  • PubMed Abstract: 

    Beta1,3-glucuronyltransferase (GlcAT-I) is an essential enzyme involved in heparan sulfate and chondroitin sulfate biosynthesis. GlcAT-I is an inverting glycosyltransferase that catalyzes the transfer of glucuronic acid (GlcUA) to the common growing linker region Galbeta1-3Galbeta1-4Xyl that is attached to a serine side chain of a core protein. Previously the structure of GlcAT-I has been solved in the presence of the donor product UDP and an acceptor analog Galbeta1-3Galbeta1-4Xyl (Pedersen, L. C., Tsuchida, K., Kitagawa, H., Sugahara, K., Darden, T. A. & Negishi, M. (2000) J. Biol. Chem. 275, 34580-34585). Here we report the x-ray crystal structure of GlcAT-I in complex with the complete donor UDP-GlcUA, thereby providing structures of an inverting glycosyltransferase in which both the complete donor and acceptor substrates are present in the active site. This structure supports the in-line displacement reaction mechanism previously proposed. It also provides information on the essential amino acid residues that determine donor substrate specificity.

    • Organizational Affiliation: 
    • Laboratory of Reproductive and Developmental Toxicology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.

Macromolecule Content 

  • Total Structure Weight: 59.25 kDa 
  • Atom Count: 4,254 
  • Modeled Residue Count: 495 
  • Deposited Residue Count: 522 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-1,3-GLUCURONYLTRANSFERASE 3
A, B
261Homo sapiensMutation(s): 0 
EC: 2.4.1.135
UniProt & NIH Common Fund Data Resources
Find proteins for O94766 (Homo sapiens)
Explore O94766 
Go to UniProtKB:  O94766
PHAROS:  O94766
GTEx:  ENSG00000149541 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94766
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.625α = 90
b = 47.978β = 93.1
c = 102.152γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description