ISDA

Entry Detail

PDB ID:

6LJL

Keywords:

LYASE

Title:

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

Biological Source:

Source Organism:

Bacteroides intestinalis DSM 17393

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2019-12-17

Release Date:

2020-12-23

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.73 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Heparinase II/III-like protein
Mutations:Y390A,H555A
Chain IDs:A
Chain Length:876
Number of Molecules:1
Biological Source:Bacteroides intestinalis DSM 17393

UniProt ID:B3C5J6 Pfam ID:PF16332, PF07940

Ligand Molecules

Primary Citation

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.Show

Nat Commun 12 1263 1263 (2021)

PMID: 33627653 DOI: 10.1038/s41467-021-21441-8

Abstact

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.

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Primary Citation of related structures