View source for 5ylk


==Complex structure of GH 113 family beta-1,4-mannanase with mannobiose==
<StructureSection load='5ylk' size='340' side='right'caption='[[5ylk]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ylk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphibacillus_xylanus_NBRC_15112 Amphibacillus xylanus NBRC 15112]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YLK FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=PRD_900115:4beta-beta-mannobiose'>PRD_900115</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=5ylk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ylk OCA], [https://pdbe.org/5ylk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ylk RCSB], [https://www.ebi.ac.uk/pdbsum/5ylk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ylk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/K0J0N5_AMPXN K0J0N5_AMPXN] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
beta-1,4-Mannanase degrades beta-1,4-mannan polymers into manno-oligosaccharides with a low degree of polymerization. To date, only one glycoside hydrolase (GH) family 113 beta-1,4-mannanase, from Alicyclobacillus acidocaldarius (AaManA) has been structurally characterized, and no complex structure of enzyme-manno-oligosaccharides from this family has been reported. Here, crystal structures of a GH family 113 beta-1,4-mannanase from Amphibacillus xylanus (AxMan113A) and its complexes with mannobiose, mannotriose, mannopentaose and mannahexaose were solved. AxMan113A had a stronger affinity for -1 and +1 mannoses, which explains why the enzyme can hydrolyze mannobiose. At least six subsites (-4 to +2) exist in the groove, but mannose units preferentially occupied subsites -4 to -1 owing to steric hindrance formed by Lys238 and Trp239. Based on the structural information and bioinformatics, rational design was implemented to enhance hydrolysis activity. Enzyme activity of AxMan113A mutants V139C, N237W, K238A and W239Y was improved by 93.7%, 63.4%, 112.9% and 36.4%, respectively, compared to the wild type. In addition, previously unreported surface binding sites were observed. Site-directed mutagenesis studies and kinetic data indicated that key residues near the surface sites play important roles in substrate binding and recognition. These first GH family 113 beta-1,4-mannanase-manno-oligosaccharide complex structures may be useful in further studying the catalytic mechanism of GH family 113 members, and provide novel insight into protein engineering of GHs to improve their hydrolysis activity.

Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus.,You X, Qin Z, Yan Q, Yang S, Li Y, Jiang Z J Biol Chem. 2018 Jun 5. pii: RA118.002363. doi: 10.1074/jbc.RA118.002363. PMID:29871927<ref>PMID:29871927</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ylk" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Amphibacillus xylanus NBRC 15112]]
[[Category: Large Structures]]
[[Category: Huang P]]
[[Category: Jiang ZQ]]
[[Category: Ma JW]]
[[Category: Yang SQ]]
[[Category: You X]]