4ucf: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ucf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum_S17 Bifidobacterium bifidum S17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UCF FirstGlance]. <br> | <table><tr><td colspan='2'>[[4ucf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum_S17 Bifidobacterium bifidum S17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UCF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=POL:N-PROPANOL'>POL</scene></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]] 1.94Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=POL:N-PROPANOL'>POL</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=4ucf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ucf OCA], [https://pdbe.org/4ucf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ucf RCSB], [https://www.ebi.ac.uk/pdbsum/4ucf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ucf ProSAT]</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=4ucf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ucf OCA], [https://pdbe.org/4ucf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ucf RCSB], [https://www.ebi.ac.uk/pdbsum/4ucf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ucf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
Latest revision as of 15:28, 20 December 2023
Crystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactoseCrystal structure of Bifidobacterium bifidum beta-galactosidase in complex with alpha-galactose
Structural highlights
Publication Abstract from PubMedIn a search for better comprehension of beta-galactosidase function and specificity, we solved the crystal structures of the GH42 beta-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with d-alpha-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with d-alpha-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two orders of magnitude decrease of the enzyme kcat without significant modification in its Km , whereas mutations Tyr289Phe and His371Phe simultaneously decreased kcat and increased Km values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with beta1-->6 and beta1-->3 bonds, while binding of the substrates with beta1-->4 linkages is less favorable. DATABASE: Structural data are available in the PDB under the accession numbers 4UZS and 4UCF. Crystal structure of beta1-->6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by alpha-galactose.,Godoy AS, Camilo CM, Kadowaki MA, Muniz HD, Espirito Santo M, Murakami MT, Nascimento AS, Polikarpov I FEBS J. 2016 Sep 29. doi: 10.1111/febs.13908. PMID:27685756[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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