1dbo

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{{Seed}}
 
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[[Image:1dbo.png|left|200px]]
 
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==CRYSTAL STRUCTURE OF CHONDROITINASE B==
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The line below this paragraph, containing "STRUCTURE_1dbo", creates the "Structure Box" on the page.
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<StructureSection load='1dbo' size='340' side='right'caption='[[1dbo]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1dbo]] 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=1DBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBO FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=G4D:4-DEOXY-ALPHA-D-GLUCOSE'>G4D</scene>, <scene name='pdbligand=GC4:4-DEOXY-D-GLUCURONIC+ACID'>GC4</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>
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{{STRUCTURE_1dbo| PDB=1dbo | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dbo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbo OCA], [https://pdbe.org/1dbo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbo RCSB], [https://www.ebi.ac.uk/pdbsum/1dbo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbo ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CSLB_PEDHD CSLB_PEDHD] Cleaves the glycosaminoglycan, dermatan sulfate.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbo_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1dbo ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===CRYSTAL STRUCTURE OF CHONDROITINASE B===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_10600383}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1dbo" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 10600383 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_10600383}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1DBO is a 1 chain structure with 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=1DBO OCA].
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==Reference==
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<ref group="xtra">PMID:10600383</ref><references group="xtra"/>
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[[Category: Pedobacter heparinus]]
[[Category: Pedobacter heparinus]]
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[[Category: Cygler, M.]]
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[[Category: Cygler M]]
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[[Category: Huang, W.]]
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[[Category: Huang W]]
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[[Category: Kim, Y S.]]
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[[Category: Kim YS]]
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[[Category: Li, Y.]]
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[[Category: Li Y]]
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[[Category: Linhardt, R J.]]
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[[Category: Linhardt RJ]]
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[[Category: Matte, A.]]
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[[Category: Matte A]]
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[[Category: Su, H.]]
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[[Category: Su H]]
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[[Category: Active site]]
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[[Category: Beta-elimination]]
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[[Category: Dematan sulfate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 22 14:49:40 2010''
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Current revision

CRYSTAL STRUCTURE OF CHONDROITINASE B

PDB ID 1dbo

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