3E80: Structure Of Heparinase Ii Complexed With Heparan Sulfate Degradation Disaccharide Product

Citation:
Abstract
Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans through a beta-elimination mechanism. Recently, we determined the crystal structure of HepII from Pedobacter heparinus (previously known as Flavobacterium heparinum) in complex with a heparin disaccharide product, and identified the location of its active site. Here we present the structure of HepII complexed with a heparan sulfate disaccharide product, proving that the same binding/active site is responsible for the degradation of both uronic acid epimers containing substrates. The key enzymatic step involves removal of a proton from the C5 carbon (a chiral center) of the uronic acid, posing a topological challenge to abstract the proton from either side of the ring in a single active site. We have identified three potential active site residues equidistant from C5 and located on both sides of the uronate product and determined their role in catalysis using a set of defined tetrasaccharide substrates. HepII H202A/Y257A mutant lost activity for both substrates and we determined its crystal structure complexed with a heparan sulfate-derived tetrasaccharide. Based on kinetic characterization of various mutants and the structure of the enzyme-substrate complex we propose residues participating in catalysis and their specific roles.
PDB ID: 3E80Download
MMDB ID: 68808
PDB Deposition Date: 2008/8/19
Updated in MMDB: 2008/12
Experimental Method:
x-ray diffraction
Resolution: 2.35  Å
Source Organism:
Similar Structures:
Biological Unit for 3E80: monomeric; determined by author and by software (PISA)
Molecular Components in 3E80
Label Count Molecule
Protein (1 molecule)
1
Heparinase II Protein
Molecule annotation
Chemicals (9 molecules)
1
1
2
1
3
1
4
1
5
1
6
4
* Click molecule labels to explore molecular sequence information.

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