6byc: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri== | ==Crystal structure of the GH2 exo-beta-mannanase from Xanthomonas axonopodis pv. citri== | ||
<StructureSection load='6byc' size='340' side='right' caption='[[6byc]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='6byc' size='340' side='right'caption='[[6byc]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6byc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYC OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6byc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_citri_pv._citri_str._306 Xanthomonas citri pv. citri str. 306]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BYC FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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]] 1.897Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=6byc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6byc OCA], [https://pdbe.org/6byc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6byc RCSB], [https://www.ebi.ac.uk/pdbsum/6byc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6byc ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8PI23_XANAC Q8PI23_XANAC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The classical microbial strategy for depolymerization of beta-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-beta-mannanases and beta-mannosidases. In this work, we describe the first exo-beta-mannanase from the GH2 family, isolated from Xanthomonas axonopodis pv. citri (XacMan2A), which can efficiently hydrolyze both manno-oligosaccharides and beta-mannan into mannose. It represents a valuable process simplification in the microbial carbon uptake that could be of potential industrial interest. Biochemical assays revealed a progressive increase in the hydrolysis rates from mannobiose to mannohexaose, which distinguishes XacMan2A from the known GH2 beta-mannosidases. Crystallographic analysis indicates that the active-site topology of XacMan2A underwent profound structural changes at the positive-subsite region, by the removal of the physical barrier canonically observed in GH2 beta-mannosidases, generating a more open and accessible active site with additional productive positive subsites. Besides that, XacMan2A contains two residue substitutions in relation to typical GH2 beta-mannosidases, Gly(439) and Gly(556), which alter the active site volume and are essential to its mode of action. Interestingly, the only other mechanistically characterized mannose-releasing exo-beta-mannanase so far is from the GH5 family, and its mode of action was attributed to the emergence of a blocking loop at the negative-subsite region of a cleft-like active site, whereas in XacMan2A, the same activity can be explained by the removal of steric barriers at the positive-subsite region in an originally pocket-like active site. Therefore, the GH2 exo-beta-mannanase represents a distinct molecular route to this rare activity, expanding our knowledge about functional convergence mechanisms in carbohydrate-active enzymes. | |||
Structural basis of exo-beta-mannanase activity in the GH2 family.,Domingues MN, Souza FHM, Vieira PS, de Morais MAB, Zanphorlin LM, Dos Santos CR, Pirolla RAS, Honorato RV, de Oliveira PSL, Gozzo FC, Murakami MT J Biol Chem. 2018 Aug 31;293(35):13636-13649. doi: 10.1074/jbc.RA118.002374. Epub, 2018 Jul 11. PMID:29997257<ref>PMID:29997257</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6byc" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Mannosidase 3D structures|Mannosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Xanthomonas citri pv. citri str. 306]] | ||
[[Category: | [[Category: Domingues MN]] | ||
[[Category: | [[Category: Morais MAB]] | ||
[[Category: | [[Category: Murakami MT]] | ||
[[Category: | [[Category: Vieira PS]] | ||