2fut
From Proteopedia
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| - | [[Image:2fut.gif|left|200px]] | + | [[Image:2fut.gif|left|200px]] |
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| - | '''Crystal Structure of Heparinase II Complexed with a Disaccharide Product''' | + | {{Structure |
| + | |PDB= 2fut |SIZE=350|CAPTION= <scene name='initialview01'>2fut</scene>, resolution 2.30Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=H1S:HEPARIN DISACCHARIDE I-S'>H1S</scene> | ||
| + | |ACTIVITY= | ||
| + | |GENE= hep B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=984 Pedobacter heparinus]) | ||
| + | }} | ||
| + | |||
| + | '''Crystal Structure of Heparinase II Complexed with a Disaccharide Product''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2FUT is a [ | + | 2FUT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FUT OCA]. |
==Reference== | ==Reference== | ||
| - | 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, J Biol Chem. 2006 Jun 2;281(22):15525-35. Epub 2006 Mar 24. PMID:[http:// | + | 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, J Biol Chem. 2006 Jun 2;281(22):15525-35. Epub 2006 Mar 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16565082 16565082] |
[[Category: Pedobacter heparinus]] | [[Category: Pedobacter heparinus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: alpha plus beta]] | [[Category: alpha plus beta]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:57:01 2008'' |
Revision as of 14:57, 20 March 2008
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| , resolution 2.30Å | |||||||
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| Ligands: | and | ||||||
| Gene: | hep B (Pedobacter heparinus) | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Heparinase II Complexed with a Disaccharide Product
Overview
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.
About this Structure
2FUT is a Single protein structure of sequence from Pedobacter heparinus. Full crystallographic information is available from OCA.
Reference
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, J Biol Chem. 2006 Jun 2;281(22):15525-35. Epub 2006 Mar 24. PMID:16565082
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