1ofl
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1ofl.gif|left|200px]] | + | [[Image:1ofl.gif|left|200px]] |
| - | + | ||
| - | '''CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE''' | + | {{Structure |
| + | |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> | ||
| + | |LIGAND= <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=MXZ:6-DEOXY-2-O-METHYL-ALPHA-L-GALACTOPYRANOSE'>MXZ</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Transferred_entry:_4.2.2.20 Transferred entry: 4.2.2.20], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.4 4.2.2.4] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1OFL is a [ | + | 1OFL 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=1OFL 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: Pedobacter heparinus]] | [[Category: Pedobacter heparinus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 25: | Line 34: | ||
[[Category: lyase]] | [[Category: lyase]] | ||
| - | ''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 13:10:15 2008'' |
Revision as of 11:10, 20 March 2008
| |||||||
| , resolution 1.70Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , and | ||||||
| Activity: | Transferred entry: 4.2.2.20, with EC number 4.2.2.4 | ||||||
| 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 Thu Mar 20 13:10:15 2008
Categories: Pedobacter heparinus | Single protein | Transferred entry: 4 2.2 20 | Cygler, M. | Michel, G. | BGC | CA | GLA | MXZ | Active site | Beta-elimination | Dematan sulfate | Lyase
