2Z86

Crystal structure of chondroitin polymerase from Escherichia coli strain K4 (K4CP) complexed with UDP-GlcUA and UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of chondroitin polymerase from Escherichia coli K4.

Osawa, T.Sugiura, N.Shimada, H.Hirooka, R.Tsuji, A.Shirakawa, T.Fukuyama, K.Kimura, M.Kimata, K.Kakuta, Y.

(2009) Biochem. Biophys. Res. Commun. 378: 10-14

  • DOI: 10.1016/j.bbrc.2008.08.121
  • Primary Citation of Related Structures:  2Z87

  • PubMed Abstract: 
  • Elongation of glycosaminoglycan chains, such as heparan and chondroitin, is catalyzed by bi-functional glycosyltransferases, for which both 3-dimensional structures and reaction mechanisms remain unknown. The bacterial chondroitin polymerase K4CP cat ...

    Elongation of glycosaminoglycan chains, such as heparan and chondroitin, is catalyzed by bi-functional glycosyltransferases, for which both 3-dimensional structures and reaction mechanisms remain unknown. The bacterial chondroitin polymerase K4CP catalyzes elongation of the chondroitin chain by alternatively transferring the GlcUA and GalNAc moiety from UDP-GlcUA and UDP-GalNAc to the non-reducing ends of the chondroitin chain. Here, we have determined the crystal structure of K4CP in the presence of UDP and UDP-GalNAc as well as with UDP and UDP-GlcUA. The structures consisted of two GT-A fold domains in which the two active sites were 60A apart. UDP-GalNAc and UDP-GlcUA were found at the active sites of the N-terminal and C-terminal domains, respectively. The present K4CP structures have provided the structural basis for further investigating the molecular mechanism of biosynthesis of chondroitin chain.


    Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chondroitin synthase
A, B, C, D
625Escherichia coliGene Names: kfoC
EC: 2.4.1.226, 2.4.1.175
Find proteins for Q8L0V4 (Escherichia coli)
Go to UniProtKB:  Q8L0V4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UGA
Query on UGA

Download SDF File 
Download CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID
UDP-GLUCURONIC ACID
C15 H22 N2 O18 P2
HDYANYHVCAPMJV-LXQIFKJMSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
B, C
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.092α = 90.00
b = 219.829β = 103.07
c = 85.856γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement
SnBphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-17
    Type: Advisory, Database references