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| | ==Protein crystal structure of xylanase A1 of Paenibacillus sp. JDR-2== | | ==Protein crystal structure of xylanase A1 of Paenibacillus sp. JDR-2== |
| - | <StructureSection load='3rdk' size='340' side='right' caption='[[3rdk]], [[Resolution|resolution]] 1.49Å' scene=''> | + | <StructureSection load='3rdk' size='340' side='right'caption='[[3rdk]], [[Resolution|resolution]] 1.49Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3rdk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paesj Paesj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3rdk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paesj Paesj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RDK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GCV:4-O-METHYL-ALPHA-D-GLUCURONIC+ACID'>GCV</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=GCV:4-O-METHYL-ALPHA-D-GLUCURONIC+ACID'>GCV</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pjdr2_0221 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=324057 PAESJ])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pjdr2_0221 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=324057 PAESJ])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=3rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rdk OCA], [http://pdbe.org/3rdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rdk RCSB], [http://www.ebi.ac.uk/pdbsum/3rdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rdk 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=3rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rdk OCA], [https://pdbe.org/3rdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rdk RCSB], [https://www.ebi.ac.uk/pdbsum/3rdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rdk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYNA1_PAESJ XYNA1_PAESJ]] Catalyzes the depolymerization of methylglucuronoxylan (MeGAXn), a beta-1,4 xylan in which 10% to 20% of the xylose residues are substituted with alpha-1,2-4-O-methylglucuronate (MeGA) residues, which is predominant in hemicellulose fractions of hardwood and crop residues. Generates xylobiose (X2) and aldotetrauronate (MeGAX3) as the predominant products of MeGAXn hydrolysis; these products are then directly assimilated by the bacterium for subsequent metabolism. Thus, allows the bacterium to efficiently use polymeric MeGAXn as a growth substrate.<ref>PMID:16461704</ref> | + | [[https://www.uniprot.org/uniprot/XYNA1_PAESJ XYNA1_PAESJ]] Catalyzes the depolymerization of methylglucuronoxylan (MeGAXn), a beta-1,4 xylan in which 10% to 20% of the xylose residues are substituted with alpha-1,2-4-O-methylglucuronate (MeGA) residues, which is predominant in hemicellulose fractions of hardwood and crop residues. Generates xylobiose (X2) and aldotetrauronate (MeGAX3) as the predominant products of MeGAXn hydrolysis; these products are then directly assimilated by the bacterium for subsequent metabolism. Thus, allows the bacterium to efficiently use polymeric MeGAXn as a growth substrate.<ref>PMID:16461704</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Endo-1,4-beta-xylanase]] | | [[Category: Endo-1,4-beta-xylanase]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Paesj]] | | [[Category: Paesj]] |
| | [[Category: John, F J.St]] | | [[Category: John, F J.St]] |
| Structural highlights
3rdk is a 2 chain structure with sequence from Paesj. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , |
| Gene: | Pjdr2_0221 (PAESJ) |
| Activity: | Endo-1,4-beta-xylanase, with EC number 3.2.1.8 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[XYNA1_PAESJ] Catalyzes the depolymerization of methylglucuronoxylan (MeGAXn), a beta-1,4 xylan in which 10% to 20% of the xylose residues are substituted with alpha-1,2-4-O-methylglucuronate (MeGA) residues, which is predominant in hemicellulose fractions of hardwood and crop residues. Generates xylobiose (X2) and aldotetrauronate (MeGAX3) as the predominant products of MeGAXn hydrolysis; these products are then directly assimilated by the bacterium for subsequent metabolism. Thus, allows the bacterium to efficiently use polymeric MeGAXn as a growth substrate.[1]
Publication Abstract from PubMed
The Gram-positive bacterium Paenibacillus sp. JDR-2 (PbJDR2) has been shown to have novel properties in the utilization of the abundant but chemically complex hemicellulosic sugar glucuronoxylan. Xylanase A1 of PbJDR2 (PbXynA1) has been implicated in an efficient process in which extracellular depolymerization of this polysaccharide is coupled to assimilation and intracellular metabolism. PbXynA1is a 154kDa cell wall anchored multimodular glycosyl hydrolase family 10 (GH10) xylanase. In this work, the 38kDa catalytic module of PbXynA1 has been structurally characterized revealing several new features not previously observed in structures of GH10 xylanases. These features are thought to facilitate hydrolysis of highly substituted, chemically complex xylans that may be the form found in close proximity to the cell wall of PbJDR2, an organism shown to have a preference for growth on polymeric glucuronoxylan.
Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2.,St John FJ, Preston JF, Pozharski E J Struct Biol. 2012 Sep 18. pii: S1047-8477(12)00249-3. doi:, 10.1016/j.jsb.2012.09.007. PMID:23000703[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Stjohn FJ, Rice JD, Preston JF. Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization. Appl Environ Microbiol. 2006 Feb;72(2):1496-506. PMID:16461704 doi:http://dx.doi.org/72/2/1496
- ↑ St John FJ, Preston JF, Pozharski E. Novel structural features of xylanase A1 from Paenibacillus sp. JDR-2. J Struct Biol. 2012 Sep 18. pii: S1047-8477(12)00249-3. doi:, 10.1016/j.jsb.2012.09.007. PMID:23000703 doi:http://dx.doi.org/10.1016/j.jsb.2012.09.007
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