3vt0: Difference between revisions

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<StructureSection load='3vt0' size='340' side='right'caption='[[3vt0]], [[Resolution|resolution]] 2.91&Aring;' scene=''>
<StructureSection load='3vt0' size='340' side='right'caption='[[3vt0]], [[Resolution|resolution]] 2.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3vt0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acet2 Acet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VT0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3vt0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VT0 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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]] 2.913&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vsf|3vsf]], [[3vsz|3vsz]], [[3vt1|3vt1]], [[3vt2|3vt2]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900004:beta-lactose'>PRD_900004</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cthe_0661 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 ACET2])</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=3vt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vt0 OCA], [https://pdbe.org/3vt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vt0 RCSB], [https://www.ebi.ac.uk/pdbsum/3vt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vt0 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=3vt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vt0 OCA], [https://pdbe.org/3vt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vt0 RCSB], [https://www.ebi.ac.uk/pdbsum/3vt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vt0 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A3DD67_ACET2 A3DD67_ACET2]
Glycoside hydrolase family 43 (GH43) consists of a variety of enzymes distributed widely in prokaryotes and eukaryotes. The mechanism by which GH43 enzymes hydrolyze oligosaccharides requires three essential acidic amino acid residues. However, one of them is thought to be missing in galactan beta-1,3-galactosidases from the GH43 family. Ct1,3Gal43A, from Clostridium thermocellum, is comprised of a GH43 domain, a CBM13 domain, and a dockerin domain and exhibits an unusual ability to hydrolyze beta-1,3-galactan in the presence of a beta-1,6 linked branch. Here, we present its crystal structure at 2.7 A resolution and complex structures of the enzyme with several substrates and analogs. Two modes of substrate binding were observed at the beta site of the CtCBM13 domain, and one galactobiose molecule was found in an "L" shaped pocket of the CtGH43 domain, which appears large enough to accommodate two more galactose units. In addition, we found that mutating Glu112 to Gln or Ala eliminated the galactan hydrolysis activity of Ct1,3Gal43A while did not disrupt its ligand binding ability. Combining this results and the crystal structure we identified Glu112 in Ct1,3Gal43A as the 'missing' essential acidic residue in galactan beta-1,3-galactosidases. Structural information presented here also suggests a mechanism by which Ct1,3Gal43A bypasses beta-1,6 linked branches in the substrate and another mechanism by which the substrate is delivered 'in trans' from the CBM13 domain to the catalytic GH43 domain.
 
Crystal structure of 1,3Gal43A, an exo-beta-1,3-galactanase from Clostridium thermocellum.,Jiang D, Fan J, Wang X, Zhao Y, Huang B, Liu J, Zhang XC J Struct Biol. 2012 Dec;180(3):447-57. doi: 10.1016/j.jsb.2012.08.005. Epub 2012 , Aug 29. PMID:22960181<ref>PMID:22960181</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3vt0" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ricin 3D structures|Ricin 3D structures]]
*[[Ricin 3D structures|Ricin 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Acet2]]
[[Category: Acetivibrio thermocellus ATCC 27405]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Fan, J]]
[[Category: Fan J]]
[[Category: Huang, B]]
[[Category: Huang B]]
[[Category: Jiang, D]]
[[Category: Jiang D]]
[[Category: Wang, X]]
[[Category: Wang X]]
[[Category: Zhang, X C]]
[[Category: Zhang XC]]
[[Category: Zhao, Y]]
[[Category: Zhao Y]]
[[Category: Cbm13]]
[[Category: Galactan hydrolysis]]
[[Category: Gh43]]
[[Category: Sugar binding protein]]

Latest revision as of 11:41, 20 March 2024

Crystal structure of Ct1,3Gal43A in complex with lactoseCrystal structure of Ct1,3Gal43A in complex with lactose

Structural highlights

3vt0 is a 6 chain structure with sequence from Acetivibrio thermocellus ATCC 27405. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.913Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A3DD67_ACET2

See Also

3vt0, resolution 2.91Å

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