Structural glycobiology of heparinase II from Pedobacter heparinus

@article{Fernandes2014StructuralGO,
  title={Structural glycobiology of heparinase II from Pedobacter heparinus},
  author={C. L. Fernandes and Gabriela B. Escouto and H. Verli},
  journal={Journal of Biomolecular Structure and Dynamics},
  year={2014},
  volume={32},
  pages={1092 - 1102}
}
The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four systems were simulated, encompassing nonglycosylated hepII without structural ions, nonglycosylated hepII with Zn2+, nonglycosylated hepII with Ca2+, and glycosylated hepII with Zn2… Expand
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References

SHOWING 1-10 OF 72 REFERENCES
Heparinase I from Flavobacterium heparinum
TLDR
It is shown that the alteration of the positive charge of the HB-1 region has a pronounced effect on heparinase I activity, and it is proposed that the positively chargedHeparin binding domain provides the necessary microenvironment for the catalytic domain of hepar inase I. Expand
Crystallization and preliminary X-ray analysis of heparinase II from Pedobacter heparinus.
TLDR
There are two molecules in the asymmetric unit, consistent with the finding that recombinant heparinase II functions as a dimer in solution. Expand
Crystal Structure of Heparinase II from Pedobacter heparinus and Its Complex with a Disaccharide Product*
TLDR
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. Expand
Catalytic Mechanism of Heparinase II Investigated by Site-directed Mutagenesis and the Crystal Structure with Its Substrate*
TLDR
The structure of HepII complexed with a heparan sulfate disaccharide product is presented, proving that the same binding/active site is responsible for the degradation of both uronic acid epimers containing substrates and proposing residues participating in catalysis and their specific roles. Expand
The Calcium-binding Sites of Heparinase I fromFlavobacterium heparinum Are Essential for Enzymatic Activity*
TLDR
A model for calcium binding to heparinase I is proposed that includes both CB-1 and CB-2 providing critical interactions, albeit via a different mechanism, and calcium may play a role in the catalytic mechanism and/or in the exolytic processive mechanism of hepar in-like glycosaminoglycan depolymerization by heparInase I. Expand
Heparins and heparan sulfates . Structure , distribution and protein interactions
Sulfated glycosaminoglycans are absent in protista, plantae and fungi. In the animal kingdom, the appearance of heparan sulfate coincides with the emergence of eumetazoa, which are animals thatExpand
Heparinase II from Flavobacterium heparinum
TLDR
It was found that one of the three cysteines in heparinase II is surface-accessible and possesses unusual chemical reactivity toward cysteine-specific chemical modifying reagents, and it was shown thatCysteine 348 is required for heparInase II activity toward hepar in but is not essential for the breakdown of heparan sulfate. Expand
Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulations.
TLDR
Results show that MD simulations could be used to characterize and quantify the interaction of synthetic compounds with AT, predicting its specific capacity to induce conformational changes in AT structure. Expand
Conformation of sulfated galactan and sulfated fucan in aqueous solutions: implications to their anticoagulant activities.
TLDR
A conformational analysis of a 2-sulfated, 3-linked alpha-L-galactan and of a alpha- L-fucan with similar structure indicates extremely different orientations for the two polysaccharides, which well correlates and explain their distinct anticoagulant activities. Expand
Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases.
TLDR
Close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin, with data indicating a dissimilar binding mode in the monomeric and oligomeric states. Expand
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