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3t08

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Current revision (09:58, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3t08' size='340' side='right'caption='[[3t08]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3t08' size='340' side='right'caption='[[3t08]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3t08]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T08 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3t08]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T08 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IPT:ISOPROPYL-1-BETA-D-THIOGALACTOSIDE'>IPT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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</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&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sep|3sep]], [[1dp0|1dp0]], [[3t0d|3t0d]], [[3t09|3t09]], [[3t0a|3t0a]], [[3t0b|3t0b]], [[3t2o|3t2o]], [[3t2p|3t2p]], [[3t2q|3t2q]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IPT:ISOPROPYL-1-BETA-D-THIOGALACTOSIDE'>IPT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0344, JW0335, lacZ ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t08 OCA], [https://pdbe.org/3t08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t08 RCSB], [https://www.ebi.ac.uk/pdbsum/3t08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t08 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=3t08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t08 OCA], [https://pdbe.org/3t08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t08 RCSB], [https://www.ebi.ac.uk/pdbsum/3t08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t08 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/BGAL_ECOLI BGAL_ECOLI]
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A loop (residues 794-803) at the active site of beta-galactosidase (Escherichia coli) opens and closes during catalysis. The alpha and beta carbons of Ser-796 form a hydrophobic connection to Phe-601 when the loop is closed while a connection via two H-bonds with the Ser hydroxyl occurs with the loop open. beta-Galactosidases with substitutions for Ser-796 were investigated. Replacement by Ala strongly stabilizes the closed conformation because of greater hydrophobicity and loss of H-bonding ability while replacement with Thr stabilizes the open form through hydrophobic interactions with its methyl group. Upon substitution with Asp much of the defined loop structure is lost. The different open-closed equilibria cause differences in the stabilities of the enzyme.substrate and enzyme.transition state complexes and of the covalent intermediate that affect the activation thermodynamics. With Ala, large changes of both the galactosylation (k(2)) and degalactosylation (k(3)) rates occur. With Thr and Asp, the k(2) and k(3) were not changed as much but large DeltaH(double dagger) and TDeltaS(double dagger) changes showed that the substitutions caused mechanistic changes. Overall, the hydrophobic and H-bonding properties of Ser-796 result in interactions strong enough to stabilize the open or closed conformations of the loop but weak enough to allow loop movement during the reaction.
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Ser-796 of beta-galactosidase (Escherichia coli) plays a key role in maintaining a balance between the opened and closed conformations of the catalytically important active site loop.,Jancewicz LJ, Wheatley RW, Sutendra G, Lee M, Fraser ME, Huber RE Arch Biochem Biophys. 2012 Jan 15;517(2):111-22. Epub 2011 Dec 1. PMID:22155115<ref>PMID:22155115</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3t08" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Galactosidase 3D structures|Galactosidase 3D structures]]
*[[Galactosidase 3D structures|Galactosidase 3D structures]]
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Beta-galactosidase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ecoli]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Fraser, M]]
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[[Category: Fraser M]]
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[[Category: Huber, R E]]
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[[Category: Huber RE]]
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[[Category: Jancewicz, L J]]
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[[Category: Jancewicz LJ]]
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[[Category: Lee, M]]
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[[Category: Lee M]]
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[[Category: Sutendra, G]]
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[[Category: Sutendra G]]
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[[Category: Wheatley, R W]]
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[[Category: Wheatley RW]]
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[[Category: Beta supersandwich]]
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[[Category: Dynampic loop conformation]]
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[[Category: Glycosidase]]
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[[Category: Hydrolase]]
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[[Category: Jelly-roll barrel]]
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[[Category: Ser-796]]
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Current revision

E. coli (LacZ) beta-galactosidase (S796A) IPTG complex

PDB ID 3t08

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