4tz3: Difference between revisions
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==Ensemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose== | ==Ensemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose== | ||
<StructureSection load='4tz3' size='340' side='right' caption='[[4tz3]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='4tz3' size='340' side='right'caption='[[4tz3]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4tz3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TZ3 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4tz3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._SirexAA-E Streptomyces sp. SirexAA-E]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TZ3 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tz3 OCA], [https://pdbe.org/4tz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tz3 RCSB], [https://www.ebi.ac.uk/pdbsum/4tz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tz3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/LAM55_STREK LAM55_STREK] Exo-beta-1,3-glucanase that specifically hydrolyzes laminarin and laminarioligosaccharides, producing glucose and laminaribiose as end products.<ref>PMID:25752603</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Carbohydrate Active Enzyme (CaZY) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-beta -1,3-glucanases. The founding structure of the GH55 is PcLam55A from the white-rot fungus Phanaerochaete chrysosporium (Ishida, T., et al. (2009) J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies implicate Glu502 as the catalytic acid (as proposed earlier for Glu663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ~30% of the GH55 family gave 34 active enzymes (19% functional coverage of the non-redundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities, and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate GH phylogenetic space for functional properties. | |||
Active site and laminarin binding in glycoside hydrolase family 55.,Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, Fox BG J Biol Chem. 2015 Mar 9. pii: jbc.M114.623579. PMID:25752603<ref>PMID:25752603</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4tz3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Streptomyces sp. SirexAA-E]] | ||
[[Category: Bergeman LF]] | |||
[[Category: Bianchetti CM]] | |||
[[Category: | [[Category: Fox BG]] | ||
[[Category: | [[Category: Takasuka TE]] | ||
[[Category: | [[Category: Yik EJ]] | ||
[[Category: | |||
[[Category: | |||
Latest revision as of 10:24, 27 September 2023
Ensemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraoseEnsemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose
Structural highlights
FunctionLAM55_STREK Exo-beta-1,3-glucanase that specifically hydrolyzes laminarin and laminarioligosaccharides, producing glucose and laminaribiose as end products.[1] Publication Abstract from PubMedThe Carbohydrate Active Enzyme (CaZY) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-beta -1,3-glucanases. The founding structure of the GH55 is PcLam55A from the white-rot fungus Phanaerochaete chrysosporium (Ishida, T., et al. (2009) J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies implicate Glu502 as the catalytic acid (as proposed earlier for Glu663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ~30% of the GH55 family gave 34 active enzymes (19% functional coverage of the non-redundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities, and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate GH phylogenetic space for functional properties. Active site and laminarin binding in glycoside hydrolase family 55.,Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, Fox BG J Biol Chem. 2015 Mar 9. pii: jbc.M114.623579. PMID:25752603[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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