3vdc: Difference between revisions
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==E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG== | ==E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG== | ||
<StructureSection load='3vdc' size='340' side='right' caption='[[3vdc]], [[Resolution|resolution]] 2.55Å' scene=''> | <StructureSection load='3vdc' size='340' side='right' caption='[[3vdc]], [[Resolution|resolution]] 2.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3vdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VDC FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dp0|1dp0]], [[1jyx|1jyx]], [[3vd3|3vd3]], [[3vd4|3vd4]], [[3vd5|3vd5]], [[3vd7|3vd7]], [[3vd9|3vd9]], [[3vda|3vda]], [[3vdb|3vdb]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dp0|1dp0]], [[1jyx|1jyx]], [[3vd3|3vd3]], [[3vd4|3vd4]], [[3vd5|3vd5]], [[3vd7|3vd7]], [[3vd9|3vd9]], [[3vda|3vda]], [[3vdb|3vdb]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lacZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lacZ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vdc RCSB], [http://www.ebi.ac.uk/pdbsum/3vdc PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdc OCA], [http://pdbe.org/3vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vdc RCSB], [http://www.ebi.ac.uk/pdbsum/3vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdc ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3vdc" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus coli migula 1895]] | |||
[[Category: Beta-galactosidase]] | [[Category: Beta-galactosidase]] | ||
[[Category: Dugdale, M L]] | [[Category: Dugdale, M L]] | ||
[[Category: Dutkoski, M J]] | [[Category: Dutkoski, M J]] | ||
Revision as of 10:04, 5 August 2016
E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTGE. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG
Structural highlights
Publication Abstract from PubMedSubstrate initially binds to beta-galactosidase (Escherichia coli) at a 'shallow' site. It then moves approximately 3A to a 'deep' site and the transition state forms. Asn460 interacts in both sites, forming a water bridge interaction with the O3 hydroxyl of the galactosyl moiety in the shallow site and a direct H-bond with the O2 hydroxyl of the transition state in the deep site. Structural and kinetic studies were done with beta-galactosidases with substitutions for Asn460. The substituted enzymes have enhanced substrate affinity in the shallow site indicating lower E.substrate complex energy levels. They have poor transition state stabilization in the deep site that is manifested by increased energy levels of the E.transition state complexes. These changes in stability result in increased activation energies and lower k(cat) values. Substrate affinity to N460D-beta-galactosidase was enhanced through greater binding enthalpy (stronger H-bonds through the bridging water) while better affinity to N460T-beta-galactosidase occurred because of greater binding entropy. The transition states are less stable with N460S- and N460T-beta-galactosidase because of the weakening or loss of the important bond to the O2 hydroxyl of the transition state. For N460D-beta-galactosidase, the transition state is less stable due to an increased entropy penalty. Substitution for Asn460 Cripples beta-galactosidase (Escherichia coli) by increasing substrate affinity and decreasing transition state stability.,Wheatley RW, Kappelhoff JC, Hahn JN, Dugdale ML, Dutkoski MJ, Tamman SD, Fraser ME, Huber RE Arch Biochem Biophys. 2012 Mar 22;521(1-2):51-61. PMID:22446164[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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