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| - | ==NATIVE BACILLUS SUBTILIS ARABINANASE ARB43A== | + | |
| - | <StructureSection load='1uv4' size='340' side='right' caption='[[1uv4]], [[Resolution|resolution]] 1.50Å' scene=''> | + | ==Native Bacillus subtilis Arabinanase Arb43A== |
| | + | <StructureSection load='1uv4' size='340' side='right'caption='[[1uv4]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1uv4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UV4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1uv4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UV4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.5Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Arabinan_endo-1,5-alpha-L-arabinosidase Arabinan endo-1,5-alpha-L-arabinosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.99 3.2.1.99] </span></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=EDO:1,2-ETHANEDIOL'>EDO</scene></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=1uv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uv4 OCA], [http://pdbe.org/1uv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1uv4 PDBsum]</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=1uv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uv4 OCA], [https://pdbe.org/1uv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1uv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uv4 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/EABN1_BACSU EABN1_BACSU]] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of linear 1,5-alpha-L-arabinan and of branched sugar beet arabinan. It displays no activity against heavily substituted arabinans or a range of other polysaccharides (larch wood arabinogalactan, wheat arabinoxylan and p-nitrophenyl-alpha-L-arabinofuranoside). The enzyme activity is progressively reduced as alpha-(1->5)-chains become shorter or more highly substituted.<ref>PMID:14973026</ref> <ref>PMID:15556708</ref> <ref>PMID:15708971</ref> | + | [https://www.uniprot.org/uniprot/EABN1_BACSU EABN1_BACSU] Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of linear 1,5-alpha-L-arabinan and of branched sugar beet arabinan. It displays no activity against heavily substituted arabinans or a range of other polysaccharides (larch wood arabinogalactan, wheat arabinoxylan and p-nitrophenyl-alpha-L-arabinofuranoside). The enzyme activity is progressively reduced as alpha-(1->5)-chains become shorter or more highly substituted.<ref>PMID:14973026</ref> <ref>PMID:15556708</ref> <ref>PMID:15708971</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uv/1uv4_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uv/1uv4_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> |
| - | </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/chain_selection.php?pdb_ID=2ata 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=1uv4 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | ==See Also== | | ==See Also== |
| - | *[[Arabinanase|Arabinanase]] | + | *[[Arabinanase 3D structures|Arabinanase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Arabinan endo-1,5-alpha-L-arabinosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Davies, G J]] | + | [[Category: Davies GJ]] |
| - | [[Category: Gilbert, H J]] | + | [[Category: Gilbert HJ]] |
| - | [[Category: Nurizzo, D]] | + | [[Category: Nurizzo D]] |
| - | [[Category: Taylor, E J]] | + | [[Category: Taylor EJ]] |
| - | [[Category: Catalysis]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Propeller]]
| + | |
| Structural highlights
Function
EABN1_BACSU Involved in the degradation of arabinan and is a key enzyme in the complete degradation of the plant cell wall. Catalyzes the internal cleavage of alpha-(1->5)-L-arabinofuranosyl residues of linear 1,5-alpha-L-arabinan and of branched sugar beet arabinan. It displays no activity against heavily substituted arabinans or a range of other polysaccharides (larch wood arabinogalactan, wheat arabinoxylan and p-nitrophenyl-alpha-L-arabinofuranoside). The enzyme activity is progressively reduced as alpha-(1->5)-chains become shorter or more highly substituted.[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
Enzymes acting on polymeric substrates are frequently classified as exo or endo, reflecting their preference for, or ignorance of, polymer chain ends. Most biotechnological applications, especially in the field of polysaccharide degradation, require either endo- or exo-acting hydrolases, or they harness the essential synergy between these two modes of action. Here, we have used genomic data in tandem with structure to modify, radically, the chain-end specificity of the Cellvibrio japonicus exo-arabinanase CjArb43A. The structure of Bacillus subtilis endo-arabinanase 43A (BsArb43A) in harness with chain-end recognition kinetics of CjArb43A directed a rational design approach that led to the conversion of the Cellvibrio enzyme from an exo to an endo mode of action. One of the exo-acting mutants, D35L/Q316A, displays similar activity to WT CjArb43A and the removal of the steric block mediated by the side chains of Gln-316 and Asp-53 at the -3 subsite confers its capacity to attack internal glycoside bonds. This study provides a template for the production of tailored industrial catalysts. The introduction of subtle changes informed by comparative 3D structural and genomic data can lead to fundamental changes in the mode of action of these enzymes.
Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A.,Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Raposo MP, Inacio JM, Mota LJ, de Sa-Nogueira I. Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis. J Bacteriol. 2004 Mar;186(5):1287-96. PMID:14973026
- ↑ Leal TF, de Sa-Nogueira I. Purification, characterization and functional analysis of an endo-arabinanase (AbnA) from Bacillus subtilis. FEMS Microbiol Lett. 2004 Dec 1;241(1):41-8. PMID:15556708 doi:http://dx.doi.org/S0378-1097(04)00721-9
- ↑ Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ. Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971
- ↑ Proctor MR, Taylor EJ, Nurizzo D, Turkenburg JP, Lloyd RM, Vardakou M, Davies GJ, Gilbert HJ. Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2697-702. Epub 2005 Feb 11. PMID:15708971
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