1of1
From Proteopedia
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| - | [[Image:1of1.jpg|left|200px]] | + | [[Image:1of1.jpg|left|200px]] |
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| - | '''KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE''' | + | {{Structure |
| + | |PDB= 1of1 |SIZE=350|CAPTION= <scene name='initialview01'>1of1</scene>, resolution 1.95Å | ||
| + | |SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Chain+B'>AC1</scene> | ||
| + | |LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=SCT:(SOUTH)-METHANOCARBA-THYMIDINE'>SCT</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Thymidine_kinase Thymidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.21 2.7.1.21] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1OF1 is a [ | + | 1OF1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_4 Human herpesvirus 4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OF1 OCA]. |
==Reference== | ==Reference== | ||
| - | The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery., Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M, J Biol Chem. 2004 Jul 30;279(31):32882-96. Epub 2004 May 21. PMID:[http:// | + | The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery., Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M, J Biol Chem. 2004 Jul 30;279(31):32882-96. Epub 2004 May 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15155751 15155751] |
[[Category: Human herpesvirus 4]] | [[Category: Human herpesvirus 4]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''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 13:09:56 2008'' |
Revision as of 11:09, 20 March 2008
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| , resolution 1.95Å | |||||||
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| Sites: | |||||||
| Ligands: | and | ||||||
| Activity: | Thymidine kinase, with EC number 2.7.1.21 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE
Overview
Chondroitinase B from Pedobacter heparinus is the only known enzyme strictly specific for dermatan sulfate and is a widely used enzymatic tool for the structural characterization of glycosaminoglycans. This beta-helical polysaccharide lyase belongs to family PL-6 and cleaves the beta(1,4) linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides as the product. The previously reported structure of its complex with a dermatan sulfate disaccharide product identified the -1 and -2 subsites of the catalytic groove. We present here the structure of chondroitinase B complexed with several dermatan sulfate and chondroitin sulfate oligosaccharides. In particular, the soaking of chondroitinase B crystals with a dermatan sulfate hexasaccharide results in a complex with two dermatan sulfate disaccharide reaction products, enabling the identification of the +2 and +1 subsites. Unexpectedly, this structure revealed the presence of a calcium ion coordinated by sequence-conserved acidic residues and by the carboxyl group of the l-iduronic acid at the +1 subsite. Kinetic and site-directed mutagenesis experiments have subsequently demonstrated that chondroitinase B absolutely requires calcium for its activity, indicating that the protein-Ca(2+)-oligosaccharide complex is functionally relevant. Modeling of an intact tetrasaccharide in the active site of chondroitinase B provided a better understanding of substrate specificity and the role of Ca(2+) in enzymatic activity. Given these results, we propose that the Ca(2+) ion neutralizes the carboxyl moiety of the l-iduronic acid at the cleavage site, whereas the conserved residues Lys-250 and Arg-271 act as Bronsted base and acid, respectively, in the lytic degradation of dermatan sulfate by chondroitinase B.
About this Structure
1OF1 is a Single protein structure of sequence from Human herpesvirus 4. Full crystallographic information is available from OCA.
Reference
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery., Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M, J Biol Chem. 2004 Jul 30;279(31):32882-96. Epub 2004 May 21. PMID:15155751
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