1DBG

CRYSTAL STRUCTURE OF CHONDROITINASE B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution.

Huang, W.Matte, A.Li, Y.Kim, Y.S.Linhardt, R.J.Su, H.Cygler, M.

(1999) J.Mol.Biol. 294: 1257-1269

  • DOI: 10.1006/jmbi.1999.3292
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycosaminoglycans (GAGs) are a family of acidic heteropolysaccharides, including such molecules as chondroitin sulfate, dermatan sulfate, heparin and keratan sulfate. Cleavage of the O-glycosidic bond within GAGs can be accomplished by hydrolases as ...

    Glycosaminoglycans (GAGs) are a family of acidic heteropolysaccharides, including such molecules as chondroitin sulfate, dermatan sulfate, heparin and keratan sulfate. Cleavage of the O-glycosidic bond within GAGs can be accomplished by hydrolases as well as lyases, yielding disaccharide and oligosaccharide products. We have determined the crystal structure of chondroitinase B, a glycosaminoglycan lyase from Flavobacterium heparinum, as well as its complex with a dermatan sulfate disaccharide product, both at 1.7 A resolution. Chondroitinase B adopts the right-handed parallel beta-helix fold, found originally in pectate lyase and subsequently in several polysaccharide lyases and hydrolases. Sequence homology between chondroitinase B and a mannuronate lyase from Pseudomonas sp. suggests this protein also adopts the beta-helix fold. Binding of the disaccharide product occurs within a positively charged cleft formed by loops extending from the surface of the beta-helix. Amino acid residues responsible for recognition of the disaccharide, as well as potential catalytic residues, have been identified. Two arginine residues, Arg318 and Arg364, are found to interact with the sulfate group attached to O-4 of N-acetylgalactosamine. Cleavage of dermatan sulfate likely occurs at the reducing end of the disaccharide, with Glu333 possibly acting as the general base.


    Organizational Affiliation

    Biotechnology Research Institute, 6100 Royalmount Ave., Montréal, Quebéc, H4P 2R2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHONDROITINASE B
A
506Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3)Mutation(s): 0 
Gene Names: cslB
EC: 4.2.2.19
Find proteins for Q46079 (Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3))
Go to UniProtKB:  Q46079
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MXY
Query on MXY

Download SDF File 
Download CCD File 
A
2-O-METHYL FUCOSE
C7 H14 O5
YLAMTMNJXPWCQN-XUVCUMPTSA-N
 Ligand Interaction
RAM
Query on RAM

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Download CCD File 
A
ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GCU
Query on GCU

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Download CCD File 
A
D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-WAXACMCWSA-N
 Ligand Interaction
G4D
Query on G4D

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Download CCD File 
A
4-DEOXY-ALPHA-D-GLUCOSE
C6 H12 O5
HDEMQQHXNOJATE-AZGQCCRYSA-N
 Ligand Interaction
XYP
Query on XYP

Download SDF File 
Download CCD File 
A
BETA-D-XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.600α = 90.00
b = 74.400β = 92.90
c = 58.700γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation