1of1
From Proteopedia
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| - | [[Image:1of1.jpg|left|200px]]<br /><applet load="1of1" size=" | + | [[Image:1of1.jpg|left|200px]]<br /><applet load="1of1" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1of1, resolution 1.95Å" /> | caption="1of1, resolution 1.95Å" /> | ||
'''KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE'''<br /> | '''KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1OF1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_4 Human herpesvirus 4] with SO4 and SCT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Site: <scene name='pdbsite=AC1:So4 Binding Site For Chain B'>AC1</scene>. Full crystallographic information is available from [http:// | + | 1OF1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_herpesvirus_4 Human herpesvirus 4] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=SCT:'>SCT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Site: <scene name='pdbsite=AC1:So4+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OF1 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:57:14 2008'' |
Revision as of 07:57, 3 February 2008
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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 with and as ligands. Active as Thymidine kinase, with EC number 2.7.1.21 Known structural/functional Site: . 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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