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| | ==Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS== | | ==Crystal Structure of Endo-1,5-alpha-L-arabinanase from Thermotoga petrophila RKU-1 in complex with TRIS== |
| - | <StructureSection load='4kc8' size='340' side='right' caption='[[4kc8]], [[Resolution|resolution]] 1.76Å' scene=''> | + | <StructureSection load='4kc8' size='340' side='right'caption='[[4kc8]], [[Resolution|resolution]] 1.76Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4kc8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thep1 Thep1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KC8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4kc8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_petrophila_RKU-1 Thermotoga petrophila RKU-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KC8 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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> | + | </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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4kc7|4kc7]], [[4kca|4kca]], [[4kcb|4kcb]]</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=4kc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kc8 OCA], [https://pdbe.org/4kc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kc8 RCSB], [https://www.ebi.ac.uk/pdbsum/4kc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kc8 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tpet_0637 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=390874 THEP1])</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='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=4kc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kc8 OCA], [http://pdbe.org/4kc8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kc8 RCSB], [http://www.ebi.ac.uk/pdbsum/4kc8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kc8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/EABN_THEP1 EABN_THEP1]] 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 in different arabinan-containing polysaccharides, and releases arabinotriose and arabinobiose as end products. It acts on branched arabinan (from sugar beet), but more slowly when compared to linear or debranched arabinan. | + | [https://www.uniprot.org/uniprot/EABN_THEP1 EABN_THEP1] 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 in different arabinan-containing polysaccharides, and releases arabinotriose and arabinobiose as end products. It acts on branched arabinan (from sugar beet), but more slowly when compared to linear or debranched arabinan. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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: Arabinan endo-1,5-alpha-L-arabinosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Thep1]] | + | [[Category: Thermotoga petrophila RKU-1]] |
| - | [[Category: Costa, M C.M F]] | + | [[Category: Costa MCMF]] |
| - | [[Category: Mesa, A N]] | + | [[Category: Mesa AN]] |
| - | [[Category: Murakami, M T]] | + | [[Category: Murakami MT]] |
| - | [[Category: Nascimento, A F.Z]] | + | [[Category: Nascimento AFZ]] |
| - | [[Category: Polo, C C]] | + | [[Category: Polo CC]] |
| - | [[Category: Prade, R A]] | + | [[Category: Prade RA]] |
| - | [[Category: Ruller, R]] | + | [[Category: Ruller R]] |
| - | [[Category: Santos, C R]] | + | [[Category: Santos CR]] |
| - | [[Category: Squina, F M]] | + | [[Category: Squina FM]] |
| - | [[Category: Arabinanase]]
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| - | [[Category: Beta-propeller]]
| + | |
| - | [[Category: Gh43]]
| + | |
| - | [[Category: Glycoside hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
EABN_THEP1 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 in different arabinan-containing polysaccharides, and releases arabinotriose and arabinobiose as end products. It acts on branched arabinan (from sugar beet), but more slowly when compared to linear or debranched arabinan.
Publication Abstract from PubMed
Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmental friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation and catalysis of GH43 ABNs are presented. Biophysical, mutational and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically-relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg203-Ala230 loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation.
Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases.,Santos CR, Polo CC, Costa MC, Nascimento AF, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PS, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DW, Murakami MT J Biol Chem. 2014 Jan 27. PMID:24469445[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Santos CR, Polo CC, Costa MC, Nascimento AF, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PS, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DW, Murakami MT. Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem. 2014 Jan 27. PMID:24469445 doi:http://dx.doi.org/10.1074/jbc.M113.537167
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