7nit: Difference between revisions
New page: '''Unreleased structure''' The entry 7nit is ON HOLD Authors: Moroz, O.V., Blagova, E., Lebedev, A.A., Sanchez Rodriguez, F., Rigden, D.J., Tams, J.W., Wilting, R., Vester, J.K., Longhi... |
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The | ==X-ray structure of a multidomain BbgIII from Bifidobacterium bifidum== | ||
<StructureSection load='7nit' size='340' side='right'caption='[[7nit]], [[Resolution|resolution]] 2.89Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7nit]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NIT FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.89Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7nit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nit OCA], [https://pdbe.org/7nit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nit RCSB], [https://www.ebi.ac.uk/pdbsum/7nit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nit ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A415C3Q2_BIFBI A0A415C3Q2_BIFBI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
beta-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some beta-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain beta-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain beta-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective beta-galactosidase modification for industrial purposes in the future. | |||
Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions.,Moroz OV, Blagova E, Lebedev AA, Sanchez Rodriguez F, Rigden DJ, Tams JW, Wilting R, Vester JK, Longhin E, Hansen GH, Krogh KBRM, Pache RA, Davies GJ, Wilson KS Acta Crystallogr D Struct Biol. 2021 Dec 1;77(Pt 12):1564-1578. doi:, 10.1107/S2059798321010949. Epub 2021 Nov 17. PMID:34866612<ref>PMID:34866612</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7nit" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Galactosidase 3D structures|Galactosidase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Bifidobacterium bifidum]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Blagova E]] | ||
[[Category: | [[Category: Davies GJ]] | ||
[[Category: | [[Category: Krogh KBR]] | ||
[[Category: Lebedev AA]] | |||
[[Category: Longhin E]] | |||
[[Category: Moroz OV]] | |||
[[Category: Pache RA]] | |||
[[Category: Rigden DJ]] | |||
[[Category: Sanchez Rodriguez F]] | |||
[[Category: Tams JW]] | |||
[[Category: Vester JK]] | |||
[[Category: Wilson KS]] | |||
[[Category: Wilting R]] | |||
Latest revision as of 15:35, 1 February 2024
X-ray structure of a multidomain BbgIII from Bifidobacterium bifidumX-ray structure of a multidomain BbgIII from Bifidobacterium bifidum
Structural highlights
FunctionPublication Abstract from PubMedbeta-Galactosidases catalyse the hydrolysis of lactose into galactose and glucose; as an alternative reaction, some beta-galactosidases also catalyse the formation of galactooligosaccharides by transglycosylation. Both reactions have industrial importance: lactose hydrolysis is used to produce lactose-free milk, while galactooligosaccharides have been shown to act as prebiotics. For some multi-domain beta-galactosidases, the hydrolysis/transglycosylation ratio can be modified by the truncation of carbohydrate-binding modules. Here, an analysis of BbgIII, a multidomain beta-galactosidase from Bifidobacterium bifidum, is presented. The X-ray structure has been determined of an intact protein corresponding to a gene construct of eight domains. The use of evolutionary covariance-based predictions made sequence docking in low-resolution areas of the model spectacularly easy, confirming the relevance of this rapidly developing deep-learning-based technique for model building. The structure revealed two alternative orientations of the CBM32 carbohydrate-binding module relative to the GH2 catalytic domain in the six crystallographically independent chains. In one orientation the CBM32 domain covers the entrance to the active site of the enzyme, while in the other orientation the active site is open, suggesting a possible mechanism for switching between the two activities of the enzyme, namely lactose hydrolysis and transgalactosylation. The location of the carbohydrate-binding site of the CBM32 domain on the opposite site of the module to where it comes into contact with the catalytic GH2 domain is consistent with its involvement in adherence to host cells. The role of the CBM32 domain in switching between hydrolysis and transglycosylation modes offers protein-engineering opportunities for selective beta-galactosidase modification for industrial purposes in the future. Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions.,Moroz OV, Blagova E, Lebedev AA, Sanchez Rodriguez F, Rigden DJ, Tams JW, Wilting R, Vester JK, Longhin E, Hansen GH, Krogh KBRM, Pache RA, Davies GJ, Wilson KS Acta Crystallogr D Struct Biol. 2021 Dec 1;77(Pt 12):1564-1578. doi:, 10.1107/S2059798321010949. Epub 2021 Nov 17. PMID:34866612[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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