Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate

Experimental Data Snapshot

  • Resolution: 1.73 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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This is version 1.2 of the entry. See complete history


Discovery of exolytic heparinases and their catalytic mechanism and potential application.

Zhang, Q.Cao, H.Y.Wei, L.Lu, D.Du, M.Yuan, M.Shi, D.Chen, X.Wang, P.Chen, X.L.Chi, L.Zhang, Y.Z.Li, F.

(2021) Nat Commun 12: 1263-1263

  • DOI: https://doi.org/10.1038/s41467-021-21441-8
  • Primary Citation of Related Structures:  
    6LJA, 6LJL

  • PubMed Abstract: 

    Heparinases (Hepases) are critical tools for the studies of highly heterogeneous heparin (HP)/heparan sulfate (HS). However, exolytic heparinases urgently needed for the sequencing of HP/HS chains remain undiscovered. Herein, a type of exolytic heparinases (exoHepases) is identified from the genomes of different bacteria. These exoHepases share almost no homology with known Hepases and prefer to digest HP rather than HS chains by sequentially releasing unsaturated disaccharides from their reducing ends. The structural study of an exoHepase (BIexoHep) shows that an N-terminal conserved DUF4962 superfamily domain is essential to the enzyme activities of these exoHepases, which is involved in the formation of a unique L-shaped catalytic cavity controlling the sequential digestion of substrates through electrostatic interactions. Further, several HP octasaccharides have been preliminarily sequenced by using BIexoHep. Overall, this study fills the research gap of exoHepases and provides urgently needed tools for the structural and functional studies of HP/HS chains.

  • Organizational Affiliation

    National Glycoengineering Research Center and Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparinase II/III-like protein876Bacteroides intestinalis DSM 17393Mutation(s): 2 
Gene Names: BACINT_00178
Find proteins for B3C5J6 (Bacteroides intestinalis DSM 17393)
Explore B3C5J6 
Go to UniProtKB:  B3C5J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3C5J6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
Glycosylation Resources
GlyTouCan:  G59698OW
GlyCosmos:  G59698OW
Experimental Data & Validation

Experimental Data

  • Resolution: 1.73 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.459α = 90
b = 107.851β = 90
c = 129.434γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31570071
National Natural Science Foundation of China (NSFC)China31971201

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description