3vdc: Difference between revisions

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 ==E. coli (lacZ) beta-galactosidase (N460T) in complex with IPTG==
-<StructureSection load='3vdc' size='340' side='right' caption='[[3vdc]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
+<StructureSection load='3vdc' size='340' side='right'caption='[[3vdc]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
 == Structural highlights ==
-<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>
+<table><tr><td colspan='2'>[[3vdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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 [https://proteopedia.org/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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.55&#8491;</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='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>
-<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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdc OCA], [https://pdbe.org/3vdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdc RCSB], [https://www.ebi.ac.uk/pdbsum/3vdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdc ProSAT]</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://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>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/BGAL_ECOLI BGAL_ECOLI]
-Substrate 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<ref>PMID:22446164</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3vdc" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Galactosidase|Galactosidase]]
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Beta-galactosidase]]
+[[Category: Large Structures]]
-[[Category: Dugdale, M L]]
+[[Category: Dugdale ML]]
-[[Category: Dutkoski, M J]]
+[[Category: Dutkoski MJ]]
-[[Category: Fraser, M E]]
+[[Category: Fraser ME]]
-[[Category: Hahn, J N]]
+[[Category: Hahn JN]]
-[[Category: Huber, R E]]
+[[Category: Huber RE]]
-[[Category: Kappelhoff, J C]]
+[[Category: Kappelhoff JC]]
-[[Category: Tamman, S D]]
+[[Category: Tamman SD]]
-[[Category: Wheatley, R W]]
+[[Category: Wheatley RW]]
-[[Category: 2-stage binding]]
-[[Category: Beta supersandwich]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Immunoglobulin]]
-[[Category: Jelly-roll barrel]]
-[[Category: Substrate binding]]
-[[Category: Transition state stabilization]]