6hf2: Difference between revisions
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<StructureSection load='6hf2' size='340' side='right'caption='[[6hf2]], [[Resolution|resolution]] 1.69Å' scene=''> | <StructureSection load='6hf2' size='340' side='right'caption='[[6hf2]], [[Resolution|resolution]] 1.69Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6hf2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HF2 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6hf2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baco1 Baco1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HF2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HF2 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=CL:CHLORIDE+ION'>CL</scene></td></tr> | </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=CL:CHLORIDE+ION'>CL</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BACOVA_02093 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=411476 BACO1])</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=6hf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hf2 OCA], [http://pdbe.org/6hf2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hf2 RCSB], [http://www.ebi.ac.uk/pdbsum/6hf2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hf2 ProSAT]</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=6hf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hf2 OCA], [http://pdbe.org/6hf2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hf2 RCSB], [http://www.ebi.ac.uk/pdbsum/6hf2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hf2 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The galactomannan utilization locus (BoManPUL) of the human gut bacterium Bacteroides ovatus encodes BoMan26B, a cell-surface-exposed endomannanase whose functional and structural features have been unclear. Our study now places BoMan26B in context with related enzymes and reveals the structural basis for its specificity. BoMan26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase BoMan26A of the same locus. Using galactomannan, BoMan26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface-exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of BoMan26B and the periplasmic alpha-galactosidase BoGal36A increased the rate of galactose release by about 10-fold compared with the rate without BoMan26B. The results suggested that BoMan26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by BoGal36A. A crystal structure of BoMan26B with galactosyl-mannotetraose bound in subsites -5 to -2 revealed an open and long active-site cleft with Trp-112 in subsite -5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the -4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that BoMan26A and BoMan26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B. | |||
A surface-exposed GH26 beta-mannanase from Bacteroides ovatus: Structure, role, and phylogenetic analysis of BoMan26B.,Bagenholm V, Wiemann M, Reddy SK, Bhattacharya A, Rosengren A, Logan DT, Stalbrand H J Biol Chem. 2019 Jun 7;294(23):9100-9117. doi: 10.1074/jbc.RA118.007171. Epub, 2019 Apr 18. PMID:31000630<ref>PMID:31000630</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6hf2" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Baco1]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bagenholm, V]] | [[Category: Bagenholm, V]] | ||
Latest revision as of 10:53, 6 November 2019
The structure of BoMan26B, a GH26 beta-mannanase from Bacteroides ovatusThe structure of BoMan26B, a GH26 beta-mannanase from Bacteroides ovatus
Structural highlights
Publication Abstract from PubMedThe galactomannan utilization locus (BoManPUL) of the human gut bacterium Bacteroides ovatus encodes BoMan26B, a cell-surface-exposed endomannanase whose functional and structural features have been unclear. Our study now places BoMan26B in context with related enzymes and reveals the structural basis for its specificity. BoMan26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase BoMan26A of the same locus. Using galactomannan, BoMan26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface-exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of BoMan26B and the periplasmic alpha-galactosidase BoGal36A increased the rate of galactose release by about 10-fold compared with the rate without BoMan26B. The results suggested that BoMan26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by BoGal36A. A crystal structure of BoMan26B with galactosyl-mannotetraose bound in subsites -5 to -2 revealed an open and long active-site cleft with Trp-112 in subsite -5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the -4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that BoMan26A and BoMan26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B. A surface-exposed GH26 beta-mannanase from Bacteroides ovatus: Structure, role, and phylogenetic analysis of BoMan26B.,Bagenholm V, Wiemann M, Reddy SK, Bhattacharya A, Rosengren A, Logan DT, Stalbrand H J Biol Chem. 2019 Jun 7;294(23):9100-9117. doi: 10.1074/jbc.RA118.007171. Epub, 2019 Apr 18. PMID:31000630[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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