2ccr: Difference between revisions
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== | ==Structure of Beta-1,4-Galactanase== | ||
<StructureSection load='2ccr' size='340' side='right'caption='[[2ccr]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2ccr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis Bacillus licheniformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CCR 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]] 2.3Å</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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PRD_900113:4beta-beta-galactobiose'>PRD_900113</scene>, <scene name='pdbligand=PRD_900114:4beta-beta-galactotriose'>PRD_900114</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=2ccr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ccr OCA], [https://pdbe.org/2ccr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ccr RCSB], [https://www.ebi.ac.uk/pdbsum/2ccr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ccr ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/GANB_BACLD GANB_BACLD] Involved in galactan degradation (PubMed:15312766). Degrades arabinose-free galactan to galactooligosaccharides, producing galactotetraose as the main product along with galactotriose, galactobiose, and galactose (PubMed:15312766). May hydrolyze the beta-1,4-galactan linkages of the galactan portion of arabinogalactan type I, a pectic plant polysaccharide from which most of the arabinose has been removed (By similarity).[UniProtKB:O07013]<ref>PMID:15312766</ref> | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cc/2ccr_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ccr ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Microbial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycoside hydrolases, which cover many different poly- and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis beta-1,4-galactanase and its inactive nucleophile mutant have been obtained with methyl-beta(1-->4)-galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the beta-1,4-galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a beta(1-->4)-galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite -4 to +5. In particular, this analysis newly identified a conserved beta-turn, which contributes to subsites -2 to +3. This beta-turn is unique to family 53 beta-1,4-galactanases among all clan GH-A families that have been structurally characterized and thus might be a structural signature for endo-beta-1,4-galactanase specificity. | |||
Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.,Le Nours J, De Maria L, Welner D, Jorgensen CT, Christensen LL, Borchert TV, Larsen S, Lo Leggio L Proteins. 2009 Jun;75(4):977-89. PMID:19089956<ref>PMID:19089956</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2ccr" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Beta-1%2C4-galactanase|Beta-1%2C4-galactanase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus licheniformis]] | [[Category: Bacillus licheniformis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Christensen | [[Category: Christensen LLH]] | ||
[[Category: | [[Category: De Maria L]] | ||
[[Category: | [[Category: Jorgensen CT]] | ||
[[Category: | [[Category: Larsen S]] | ||
[[Category: | [[Category: Le Nours J]] | ||
[[Category: | [[Category: Lo Leggio L]] | ||
[[Category: Welner | [[Category: Welner D]] | ||
Latest revision as of 17:13, 13 December 2023
Structure of Beta-1,4-GalactanaseStructure of Beta-1,4-Galactanase
Structural highlights
FunctionGANB_BACLD Involved in galactan degradation (PubMed:15312766). Degrades arabinose-free galactan to galactooligosaccharides, producing galactotetraose as the main product along with galactotriose, galactobiose, and galactose (PubMed:15312766). May hydrolyze the beta-1,4-galactan linkages of the galactan portion of arabinogalactan type I, a pectic plant polysaccharide from which most of the arabinose has been removed (By similarity).[UniProtKB:O07013][1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedMicrobial beta-1,4-galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH-A of glycoside hydrolases, which cover many different poly- and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis beta-1,4-galactanase and its inactive nucleophile mutant have been obtained with methyl-beta(1-->4)-galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the beta-1,4-galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a beta(1-->4)-galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite -4 to +5. In particular, this analysis newly identified a conserved beta-turn, which contributes to subsites -2 to +3. This beta-turn is unique to family 53 beta-1,4-galactanases among all clan GH-A families that have been structurally characterized and thus might be a structural signature for endo-beta-1,4-galactanase specificity. Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling.,Le Nours J, De Maria L, Welner D, Jorgensen CT, Christensen LL, Borchert TV, Larsen S, Lo Leggio L Proteins. 2009 Jun;75(4):977-89. PMID:19089956[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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