Crystal Structure of Heparinase II

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Crystal Structure of Heparinase II from Pedobacter heparinus and Its Complex with a Disaccharide Product.

Shaya, D.Tocilj, A.Li, Y.Myette, J.Venkataraman, G.Sasisekharan, R.Cygler, M.

(2006) J Biol Chem 281: 15525-15535

  • DOI: https://doi.org/10.1074/jbc.M512055200
  • Primary Citation of Related Structures:  
    2FUQ, 2FUT

  • PubMed Abstract: 

    Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism. This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase. We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), in a ligand-free state at 2.15 A resolution and in complex with a disaccharide product of heparin degradation at 2.30 A resolution. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 (PL8) enzymes chondroitin AC lyase and hyaluronate lyase. In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer. The structure of the N-terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family. A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site. The disaccharide binds in a long, deep canyon formed at the top of the N-terminal domain and by loops extending from the central domain. Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the "+1" and "+2" subsites. The structure of the enzyme-product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan-sulfate degradation.

  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
heparinase II protein
A, B
747Pedobacter heparinusMutation(s): 2 
Gene Names: hep b
Find proteins for C6XZB6 (Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3))
Explore C6XZB6 
Go to UniProtKB:  C6XZB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6XZB6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose
C, D
Glycosylation Resources
GlyTouCan:  G51375MF
GlyCosmos:  G51375MF
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.046α = 90
b = 119.339β = 90
c = 200.7γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2016-03-23
    Changes: Derived calculations, Non-polymer description
  • Version 2.0: 2019-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary