1ofl
From Proteopedia
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|PDB= 1ofl |SIZE=350|CAPTION= <scene name='initialview01'>1ofl</scene>, resolution 1.70Å | |PDB= 1ofl |SIZE=350|CAPTION= <scene name='initialview01'>1ofl</scene>, resolution 1.70Å | ||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=ASG:2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE'>ASG</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DGC:D-GLUCURONIC+ACID'>DGC</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MXZ:6-DEOXY-2-O-METHYL-ALPHA-L-GALACTOPYRANOSE'>MXZ</scene>, <scene name='pdbligand=NGK:2-(ACETYLAMINO)-2-DEOXY-4-O-SULFO-ALPHA-D-GALACTOPYRANOSE'>NGK</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=RAM:RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/ | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Chondroitin-sulfate-ABC_endolyase Chondroitin-sulfate-ABC endolyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.20 4.2.2.20] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ofl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ofl OCA], [http://www.ebi.ac.uk/pdbsum/1ofl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ofl RCSB]</span> | ||
}} | }} | ||
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==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://www.ncbi.nlm.nih.gov/pubmed/15155751 15155751] | 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: Chondroitin-sulfate-ABC endolyase]] | ||
[[Category: Pedobacter heparinus]] | [[Category: Pedobacter heparinus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Transferred entry: 4 2.2 20]] | ||
[[Category: Cygler, M.]] | [[Category: Cygler, M.]] | ||
[[Category: Michel, G.]] | [[Category: Michel, G.]] | ||
| - | [[Category: BGC]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: GLA]] | ||
| - | [[Category: MXZ]] | ||
[[Category: active site]] | [[Category: active site]] | ||
[[Category: beta-elimination]] | [[Category: beta-elimination]] | ||
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[[Category: lyase]] | [[Category: lyase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:44:40 2008'' |
Revision as of 19:44, 30 March 2008
| |||||||
| , resolution 1.70Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , , , , , , , , | ||||||
| Activity: | Chondroitin-sulfate-ABC endolyase, with EC number 4.2.2.20 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE
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
1OFL is a Single protein structure of sequence from Pedobacter heparinus. 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
Page seeded by OCA on Sun Mar 30 22:44:40 2008
