1dbg: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dbg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBG FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dbg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBG FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=G4D:4-DEOXY-ALPHA-D-GLUCOSE'>G4D</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MXY:2-O-METHYL+FUCOSE'>MXY</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=G4D:4-DEOXY-ALPHA-D-GLUCOSE'>G4D</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MXY:2-O-METHYL+FUCOSE'>MXY</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbg OCA], [https://pdbe.org/1dbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbg RCSB], [https://www.ebi.ac.uk/pdbsum/1dbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbg ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbg OCA], [https://pdbe.org/1dbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbg RCSB], [https://www.ebi.ac.uk/pdbsum/1dbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbg ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CSLB_PEDHD CSLB_PEDHD] Cleaves the glycosaminoglycan, dermatan sulfate.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dbg ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dbg ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glycosaminoglycans (GAGs) are a family of acidic heteropolysaccharides, including such molecules as chondroitin sulfate, dermatan sulfate, heparin and keratan sulfate. Cleavage of the O-glycosidic bond within GAGs can be accomplished by hydrolases as well as lyases, yielding disaccharide and oligosaccharide products. We have determined the crystal structure of chondroitinase B, a glycosaminoglycan lyase from Flavobacterium heparinum, as well as its complex with a dermatan sulfate disaccharide product, both at 1.7 A resolution. Chondroitinase B adopts the right-handed parallel beta-helix fold, found originally in pectate lyase and subsequently in several polysaccharide lyases and hydrolases. Sequence homology between chondroitinase B and a mannuronate lyase from Pseudomonas sp. suggests this protein also adopts the beta-helix fold. Binding of the disaccharide product occurs within a positively charged cleft formed by loops extending from the surface of the beta-helix. Amino acid residues responsible for recognition of the disaccharide, as well as potential catalytic residues, have been identified. Two arginine residues, Arg318 and Arg364, are found to interact with the sulfate group attached to O-4 of N-acetylgalactosamine. Cleavage of dermatan sulfate likely occurs at the reducing end of the disaccharide, with Glu333 possibly acting as the general base.
Crystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution.,Huang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, Cygler M J Mol Biol. 1999 Dec 17;294(5):1257-69. PMID:10600383<ref>PMID:10600383</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dbg" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pedobacter heparinus]]
[[Category: Pedobacter heparinus]]
[[Category: Cygler, M]]
[[Category: Cygler M]]
[[Category: Huang, W]]
[[Category: Huang W]]
[[Category: Kim, Y S]]
[[Category: Kim YS]]
[[Category: Li, Y]]
[[Category: Li Y]]
[[Category: Linhardt, R J]]
[[Category: Linhardt RJ]]
[[Category: Matte, A]]
[[Category: Matte A]]
[[Category: Su, H]]
[[Category: Su H]]
[[Category: Beta helix]]
[[Category: Dematan sulfate]]
[[Category: Lyase]]
[[Category: Polysaccharide lyase]]

Revision as of 09:49, 20 March 2024

CRYSTAL STRUCTURE OF CHONDROITINASE B

1dbg, resolution 1.70Å

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