6lcf: Difference between revisions
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==Crystal Structure of beta-L-arabinobiose binding protein - native== | ==Crystal Structure of beta-L-arabinobiose binding protein - native== | ||
<StructureSection load='6lcf' size='340' side='right'caption='[[6lcf]]' scene=''> | <StructureSection load='6lcf' size='340' side='right'caption='[[6lcf]], [[Resolution|resolution]] 1.92Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LCF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LCF FirstGlance]. <br> | <table><tr><td colspan='2'>[[6lcf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LCF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LCF FirstGlance]. <br> | ||
</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=6lcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lcf OCA], [http://pdbe.org/6lcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lcf RCSB], [http://www.ebi.ac.uk/pdbsum/6lcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lcf ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APC1462_0182, APC1476_0195, APC1503_0213, APS65_00860, BBG7_0210, BL105A_0201, DPC6316_0214, DPC6317_0191, DW237_03380, DW792_04665, DWV59_05050, DWV93_04885, DWZ73_01175, EAI75_02995, HMPREF0177_01141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216816 AS 1.2186])</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=6lcf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lcf OCA], [http://pdbe.org/6lcf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lcf RCSB], [http://www.ebi.ac.uk/pdbsum/6lcf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lcf ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for beta-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for alpha-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting beta-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the beta-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-beta1,2-Araf (beta-Ara2 ) with a Kd of 0.150 mum, but did not bind L-arabinose or methyl-beta-Ara2 . Therefore, the SBP was termed beta-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with beta-Ara2 were determined at resolutions of up to 1.78 A. The findings showed that beta-Ara2 was bound to BABP within a short tunnel between two lobes as an alpha-anomeric form at its reducing end. BABP forms extensive interactions with beta-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for beta-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/). | |||
Structural analysis of beta-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.,Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S FEBS J. 2020 Apr 4. doi: 10.1111/febs.15315. PMID:32246585<ref>PMID:32246585</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6lcf" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: As 1 2186]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Arakawa T]] | [[Category: Arakawa, T]] | ||
[[Category: Fushinobu S]] | [[Category: Fushinobu, S]] | ||
[[Category: Miyake M]] | [[Category: Miyake, M]] | ||
[[Category: Substrate-binding protein of abc transporter]] | |||
[[Category: Sugar binding protein]] | |||
Revision as of 13:48, 24 December 2020
Crystal Structure of beta-L-arabinobiose binding protein - nativeCrystal Structure of beta-L-arabinobiose binding protein - native
Structural highlights
Publication Abstract from PubMedBifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for beta-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for alpha-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting beta-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the beta-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-beta1,2-Araf (beta-Ara2 ) with a Kd of 0.150 mum, but did not bind L-arabinose or methyl-beta-Ara2 . Therefore, the SBP was termed beta-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with beta-Ara2 were determined at resolutions of up to 1.78 A. The findings showed that beta-Ara2 was bound to BABP within a short tunnel between two lobes as an alpha-anomeric form at its reducing end. BABP forms extensive interactions with beta-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for beta-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/). Structural analysis of beta-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.,Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S FEBS J. 2020 Apr 4. doi: 10.1111/febs.15315. PMID:32246585[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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