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| | <StructureSection load='2e24' size='340' side='right'caption='[[2e24]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='2e24' size='340' side='right'caption='[[2e24]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2e24]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacgl Bacgl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E24 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2e24]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._GL1 Bacillus sp. GL1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E24 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j0m|1j0m]], [[1j0n|1j0n]], [[1x1h|1x1h]], [[1x1i|1x1i]], [[1x1j|1x1j]], [[2e22|2e22]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=2e24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e24 OCA], [https://pdbe.org/2e24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e24 RCSB], [https://www.ebi.ac.uk/pdbsum/2e24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e24 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e24 OCA], [http://pdbe.org/2e24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e24 RCSB], [http://www.ebi.ac.uk/pdbsum/2e24 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2e24 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XANLY_BACGL XANLY_BACGL]] Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.<ref>PMID:10347037</ref> <ref>PMID:11157235</ref> <ref>PMID:9758797</ref> | + | [https://www.uniprot.org/uniprot/XANLY_BACGL XANLY_BACGL] Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.<ref>PMID:10347037</ref> <ref>PMID:11157235</ref> <ref>PMID:9758797</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacgl]] | + | [[Category: Bacillus sp. GL1]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Xanthan lyase]]
| + | [[Category: Hashimoto W]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Maruyama Y]] |
| - | [[Category: Maruyama, Y]] | + | [[Category: Mikami B]] |
| - | [[Category: Mikami, B]] | + | [[Category: Murata K]] |
| - | [[Category: Murata, K]] | + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Polysaccharide lyase]]
| + | |
| - | [[Category: Xanthan]]
| + | |
| Structural highlights
Function
XANLY_BACGL Plays a role in xanthan depolymerization pathway by cleaving the linkage between the terminal mannosyl and glucuronyl residues of the side chain of xanthan to liberate pyruvylated mannose.[1] [2] [3]
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
Xanthan is a bacterial heteropolysaccharide composed of pentasaccharide repeating units, i.e., a cellobiose as a backbone and a trisaccharide consisting of two mannoses and one glucuronic acid as a side chain. Nonreducing terminal mannose residues of xanthan side chains are partially pyruvated. Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8, acts specifically on pyruvated side chains of xanthan and yields pyruvated mannose through a beta-elimination reaction by using a single Tyr255 residue as base and acid catalysts. Here we show structural factors for substrate recognition by xanthan lyase through X-ray crystallographic and mutational analyses. The enzyme accommodates mannose and pyruvated mannose at the -1 subsite, although both inhibitor and dissociation constants of the two monosaccharides indicated that the affinity of pyruvated mannose for xanthan lyase is much higher than that of mannose. The high affinity of pyruvated mannose is probably due to the formation of additional hydrogen bonds between the carboxyl group of pyruvated mannose and amino acid residues of Tyr315 and Arg612. Site-directed mutagenesis of the two residues demonstrated that Arg612 is a key residue in recognizing pyruvated mannose. Arg612 is located in the protruding loop covering the substrate, suggesting that the loop functions as a lid that is responsible for the proper accommodation of the substrate at the active site.
A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan.,Maruyama Y, Mikami B, Hashimoto W, Murata K Biochemistry. 2007 Jan 23;46(3):781-91. PMID:17223699[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nankai H, Hashimoto W, Miki H, Kawai S, Murata K. Microbial system for polysaccharide depolymerization: enzymatic route for xanthan depolymerization by Bacillus sp. strain GL1. Appl Environ Microbiol. 1999 Jun;65(6):2520-6. PMID:10347037
- ↑ Hashimoto W, Miki H, Tsuchiya N, Nankai H, Murata K. Polysaccharide lyase: molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1. Appl Environ Microbiol. 2001 Feb;67(2):713-20. PMID:11157235 doi:http://dx.doi.org/10.1128/AEM.67.2.713-720.2001
- ↑ Hashimoto W, Miki H, Tsuchiya N, Nankai H, Murata K. Xanthan lyase of Bacillus sp. strain GL1 liberates pyruvylated mannose from xanthan side chains. Appl Environ Microbiol. 1998 Oct;64(10):3765-8. PMID:9758797
- ↑ Maruyama Y, Mikami B, Hashimoto W, Murata K. A structural factor responsible for substrate recognition by Bacillus sp. GL1 xanthan lyase that acts specifically on pyruvated side chains of xanthan. Biochemistry. 2007 Jan 23;46(3):781-91. PMID:17223699 doi:10.1021/bi0619775
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