|
|
| Line 3: |
Line 3: |
| | <StructureSection load='5ej3' size='340' side='right'caption='[[5ej3]], [[Resolution|resolution]] 1.31Å' scene=''> | | <StructureSection load='5ej3' size='340' side='right'caption='[[5ej3]], [[Resolution|resolution]] 1.31Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ej3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_lividans"_krasil'nikov_et_al._1965 "actinomyces lividans" krasil'nikov et al. 1965]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EJ3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ej3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans Streptomyces lividans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EJ3 FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xlnB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1916 "Actinomyces lividans" Krasil'nikov et al. 1965])</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]] 1.314Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ej3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej3 OCA], [https://pdbe.org/5ej3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ej3 RCSB], [https://www.ebi.ac.uk/pdbsum/5ej3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej3 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ej3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ej3 OCA], [http://pdbe.org/5ej3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ej3 RCSB], [http://www.ebi.ac.uk/pdbsum/5ej3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ej3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYNB_STRLI XYNB_STRLI]] Contributes to hydrolyze hemicellulose, the major component of plant cell-walls. XLNA and XLNB seem to act sequentially on the substrate to yield xylobiose and xylose as carbon sources. | + | [https://www.uniprot.org/uniprot/XYNB_STRLI XYNB_STRLI] Contributes to hydrolyze hemicellulose, the major component of plant cell-walls. XLNA and XLNB seem to act sequentially on the substrate to yield xylobiose and xylose as carbon sources. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 23: |
Line 22: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Actinomyces lividans krasil'nikov et al. 1965]] | |
| - | [[Category: Endo-1,4-beta-xylanase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Couture, J F]] | + | [[Category: Streptomyces lividans]] |
| - | [[Category: Beta-glycosidase]] | + | [[Category: Couture J-F]] |
| - | [[Category: Beta-jelly roll domain]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Xylan]]
| + | |
| - | [[Category: Xylanase b2]]
| + | |
| Structural highlights
Function
XYNB_STRLI Contributes to hydrolyze hemicellulose, the major component of plant cell-walls. XLNA and XLNB seem to act sequentially on the substrate to yield xylobiose and xylose as carbon sources.
Publication Abstract from PubMed
Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame. Here, we used nuclear magnetic resonance titration and relaxation dispersion experiments ((15)N-CPMG) in combination with X-ray crystallography and computational simulations to probe conformational motions occurring on the catalytically relevant millisecond time frame in xylanase B2 (XlnB2) and its catalytically impaired mutant E87A from Streptomyces lividans 66. Our results show distinct dynamical properties for the apo and ligand-bound states of the enzymes. The apo form of XlnB2 experiences conformational exchange for residues in the fingers and palm regions of the catalytic cleft, while the catalytically impaired E87A variant displays millisecond dynamics only in the fingers, demonstrating the long-range effect of the mutation on flexibility. Ligand binding induces enhanced conformational exchange of residues interacting with the ligand in the fingers and thumb loop regions, emphasizing the potential role of residue motions in the fingers and thumb loop regions for recognition, positioning, processivity, and/or stabilization of ligands in XlnB2. To the best of our knowledge, this work represents the first experimental characterization of millisecond dynamics in a GH11 xylanase family member. These results offer new insights into the potential role of conformational exchange in GH11 enzymes, providing essential dynamic information to help improve protein engineering and design applications.
Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans.,Gagne D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N Biochemistry. 2016 Aug 2;55(30):4184-96. doi: 10.1021/acs.biochem.6b00130. Epub, 2016 Jul 21. PMID:27387012[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gagne D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry. 2016 Aug 2;55(30):4184-96. doi: 10.1021/acs.biochem.6b00130. Epub, 2016 Jul 21. PMID:27387012 doi:http://dx.doi.org/10.1021/acs.biochem.6b00130
|
