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| | <StructureSection load='2q1f' size='340' side='right'caption='[[2q1f]], [[Resolution|resolution]] 2.85Å' scene=''> | | <StructureSection load='2q1f' size='340' side='right'caption='[[2q1f]], [[Resolution|resolution]] 2.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2q1f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2q1f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1F FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.85Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cslABC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Chondroitin-sulfate-ABC_exolyase Chondroitin-sulfate-ABC exolyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.21 4.2.2.21] </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=2q1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1f OCA], [https://pdbe.org/2q1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1f RCSB], [https://www.ebi.ac.uk/pdbsum/2q1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1f 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=2q1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1f OCA], [https://pdbe.org/2q1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1f RCSB], [https://www.ebi.ac.uk/pdbsum/2q1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1f ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/CABC2_BACTN CABC2_BACTN]] Broad-specificity glycosaminoglycan lyase, which acts in an exolytic fashion degrading chondroitin sulfates and dermatan sulfate to yield only disaccharide products. Has a preference for chondroitin 4-sulfate over chondroitin 6-sulfate. Has extremely low activity against hyaluronic acid. Is not active against acharan sulfate, heparin or heparan sulfate.[UniProtKB:C5G6D7]<ref>PMID:6630153</ref>
| + | [https://www.uniprot.org/uniprot/CABC2_BACT4 CABC2_BACT4] Broad-specificity glycosaminoglycan lyase, which acts in an exolytic fashion degrading chondroitin sulfates and dermatan sulfate to yield only disaccharide products. Has a preference for chondroitin 4-sulfate over chondroitin 6-sulfate. Has extremely low activity against hyaluronic acid. Is not active against acharan sulfate, heparin or heparan sulfate.<ref>PMID:18512954</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1f_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1f_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus thetaiotaomicron distaso 1912]] | + | [[Category: Bacteroides thetaiotaomicron]] |
| - | [[Category: Chondroitin-sulfate-ABC exolyase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cygler, M]] | + | [[Category: Cygler M]] |
| - | [[Category: Shaya, D]] | + | [[Category: Shaya D]] |
| - | [[Category: Alpha plus beta]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
CABC2_BACT4 Broad-specificity glycosaminoglycan lyase, which acts in an exolytic fashion degrading chondroitin sulfates and dermatan sulfate to yield only disaccharide products. Has a preference for chondroitin 4-sulfate over chondroitin 6-sulfate. Has extremely low activity against hyaluronic acid. Is not active against acharan sulfate, heparin or heparan sulfate.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Enzymes have evolved as catalysts with high degrees of stereospecificity. When both enantiomers are biologically important, enzymes with two different folds usually catalyze reactions with the individual enantiomers. In rare cases a single enzyme can process both enantiomers efficiently, but no molecular basis for such catalysis has been established. The family of bacterial chondroitin lyases ABC comprises such enzymes. They can degrade both chondroitin sulfate (CS) and dermatan sulfate (DS) glycosaminoglycans at the nonreducing end of either glucuronic acid (CS) or its epimer iduronic acid (DS) by a beta-elimination mechanism, which commences with the removal of the C-5 proton from the uronic acid. Two other structural folds evolved to perform these reactions in an epimer-specific fashion: (alpha/alpha)(5) for CS (chondroitin lyases AC) and beta-helix for DS (chondroitin lyases B); their catalytic mechanisms have been established at the molecular level. The structure of chondroitinase ABC from Proteus vulgaris showed surprising similarity to chondroitinase AC, including the presence of a Tyr-His-Glu-Arg catalytic tetrad, which provided a possible mechanism for CS degradation but not for DS degradation. We determined the structure of a distantly related Bacteroides thetaiotaomicron chondroitinase ABC to identify additional structurally conserved residues potentially involved in catalysis. We found a conserved cluster located approximately 12 A from the catalytic tetrad. We demonstrate that a histidine in this cluster is essential for catalysis of DS but not CS. The enzyme utilizes a single substrate-binding site while having two partially overlapping active sites catalyzing the respective reactions. The spatial separation of the two sets of residues suggests a substrate-induced conformational change that brings all catalytically essential residues close together.
Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid.,Shaya D, Hahn BS, Bjerkan TM, Kim WS, Park NY, Sim JS, Kim YS, Cygler M Glycobiology. 2008 Mar;18(3):270-7. Epub 2008 Jan 28. PMID:18227125[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shaya D, Hahn BS, Park NY, Sim JS, Kim YS, Cygler M. Characterization of chondroitin sulfate lyase ABC from Bacteroides thetaiotaomicron WAL2926. Biochemistry. 2008 Jun 24;47(25):6650-61. PMID:18512954 doi:10.1021/bi800353g
- ↑ Shaya D, Hahn BS, Bjerkan TM, Kim WS, Park NY, Sim JS, Kim YS, Cygler M. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid. Glycobiology. 2008 Mar;18(3):270-7. Epub 2008 Jan 28. PMID:18227125 doi:10.1093/glycob/cwn002
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