6gh3: Difference between revisions
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==Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1-phosphate bound== | ==Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1-phosphate bound== | ||
<StructureSection load='6gh3' size='340' side='right' caption='[[6gh3]], [[Resolution|resolution]] 1.82Å' scene=''> | <StructureSection load='6gh3' size='340' side='right'caption='[[6gh3]], [[Resolution|resolution]] 1.82Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6gh3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GH3 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6gh3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_sp._ym1 Paenibacillus sp. ym1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GH3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GH3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M1P:ALPHA-D-MANNOSE+1-PHOSPHATE'>M1P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M1P:ALPHA-D-MANNOSE+1-PHOSPHATE'>M1P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=856729 Paenibacillus sp. YM1])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Laminaribiose_phosphorylase Laminaribiose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.31 2.4.1.31] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Laminaribiose_phosphorylase Laminaribiose phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.31 2.4.1.31] </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=6gh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gh3 OCA], [http://pdbe.org/6gh3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gh3 RCSB], [http://www.ebi.ac.uk/pdbsum/6gh3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gh3 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=6gh3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gh3 OCA], [http://pdbe.org/6gh3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gh3 RCSB], [http://www.ebi.ac.uk/pdbsum/6gh3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gh3 ProSAT]</span></td></tr> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Laminaribiose phosphorylase]] | [[Category: Laminaribiose phosphorylase]] | ||
[[Category: Large Structures]] | |||
[[Category: Paenibacillus sp. ym1]] | |||
[[Category: Angulo, J]] | [[Category: Angulo, J]] | ||
[[Category: Field, R A]] | [[Category: Field, R A]] | ||
Latest revision as of 10:54, 24 April 2019
Paenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1-phosphate boundPaenibacillus sp. YM1 laminaribiose phosphorylase with alpha-man-1-phosphate bound
Structural highlights
Publication Abstract from PubMedGlycoside phosphorylases (GPs) carry out a reversible phosphorolysis of carbohydrates into oligosaccharide acceptors and the corresponding sugar 1-phosphates. The reversibility of the reaction enables the use of GPs as biocatalysts for carbohydrate synthesis. Glycosyl hydrolase family 94 (GH94), which only comprises GPs, is one of the most studied GP families that have been used as biocatalysts for carbohydrate synthesis, in academic research and in industrial production. Understanding the mechanism of GH94 enzymes is a crucial step towards enzyme engineering to improve and expand the applications of these enzymes in synthesis. In this work with a GH94 laminaribiose phosphorylase from Paenibacillus sp. YM1 (PsLBP), we have demonstrated an enzymatic synthesis of disaccharide 1 using natural acceptor glucose and non-cognate donor substrate -mannose 1-phosphate (Man1P). To investigate how the enzyme recognizes different sugar 1-phosphates, we solved the X-ray crystal structures of PsLBP in complex with Glc1P and Man1P, providing the first molecular detail of the recognition of a non-cognate donor substrate by GPs, which revealed the importance of hydrogen bonding between the active site residues and hydroxyl groups at C2, C4 and C6 of sugar 1-phosphates. Furthermore, we used STD NMR to support the crystallographic studies on the sugar 1-phosphates, as well as to provide further insights into the PsLBP recognition of the acceptors and the disaccharide products. Unravelling the relaxed specificity of laminaribiose phosphorylase from Paenibacillus sp. strain YM-1 towards mannose 1-phosphate.,Field RA, Kuhaudomlarp S, Walpole S, Stevenson C, Nepogodiev S, Lawson D, Angulo J Chembiochem. 2018 Jun 1. doi: 10.1002/cbic.201800260. PMID:29856496[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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