3pbg: Difference between revisions

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-[[Image:3pbg.jpg|left|200px]]
- {{Structure
+==6-PHOSPHO-BETA-GALACTOSIDASE FORM-C==
-|PDB= 3pbg |SIZE=350|CAPTION= <scene name='initialview01'>3pbg</scene>, resolution 2.7&Aring;
+<StructureSection load='3pbg' size='340' side='right'caption='[[3pbg]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-|SITE= <scene name='pdbsite=ACA:Catalytic+Residues'>ACA</scene>, <scene name='pdbsite=ACB:Catalytic+Residues'>ACB</scene>, <scene name='pdbsite=PHA:Phosphate+Binding+Site'>PHA</scene> and <scene name='pdbsite=PHB:Phosphate+Binding+Site'>PHB</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[3pbg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PBG FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/6-phospho-beta-galactosidase 6-phospho-beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.85 3.2.1.85] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-|GENE= LACG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1358 Lactococcus lactis])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pbg OCA], [https://pdbe.org/3pbg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pbg RCSB], [https://www.ebi.ac.uk/pdbsum/3pbg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pbg ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pbg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pbg OCA], [http://www.ebi.ac.uk/pdbsum/3pbg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3pbg RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/LACG_LACLL LACG_LACLL]
+== 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/pb/3pbg_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=3pbg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The initial structural model of 6-phospho-beta-galactosidase from Lactococcus lactis was refined to an R-factor of 16.4% (R[free] = 23.6%) to 2.3 A resolution (1 A = 0.1 nm), and the structures of three other crystal forms were solved by molecular replacement. The four structural models are essentially identical. The catalytic center of the enzyme is approximately at the mass center of the molecule and can only be reached through a 20 A long channel, which is observed with an "open" or "closed" entrance. The closed entrance is probably too small for the educt lactose-6-phosphate to enter, but large enough for the first product glucose to leave. Among the presented structures is a complex between an almost inactive mutant and the second product galactose-6-phosphate, which is exclusively bound at side-chains. A superposition (onto the native enzyme) of galactose-6-phosphate as bound to the mutant suggests the geometry of a postulated covalent intermediate. The binding mode of the educt was modeled, starting from the bound galactose-6-phosphate. A tightly fixed tryptophan is used as a chopping-board for splitting the disaccharide, and several other aromatic residues in the active center cavity are likely to participate in substrate transport/binding.
-'''6-PHOSPHO-BETA-GALACTOSIDASE FORM-C'''
+Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis.,Wiesmann C, Hengstenberg W, Schulz GE J Mol Biol. 1997 Jun 27;269(5):851-60. PMID:9223646<ref>PMID:9223646</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3pbg" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The initial structural model of 6-phospho-beta-galactosidase from Lactococcus lactis was refined to an R-factor of 16.4% (R[free] = 23.6%) to 2.3 A resolution (1 A = 0.1 nm), and the structures of three other crystal forms were solved by molecular replacement. The four structural models are essentially identical. The catalytic center of the enzyme is approximately at the mass center of the molecule and can only be reached through a 20 A long channel, which is observed with an "open" or "closed" entrance. The closed entrance is probably too small for the educt lactose-6-phosphate to enter, but large enough for the first product glucose to leave. Among the presented structures is a complex between an almost inactive mutant and the second product galactose-6-phosphate, which is exclusively bound at side-chains. A superposition (onto the native enzyme) of galactose-6-phosphate as bound to the mutant suggests the geometry of a postulated covalent intermediate. The binding mode of the educt was modeled, starting from the bound galactose-6-phosphate. A tightly fixed tryptophan is used as a chopping-board for splitting the disaccharide, and several other aromatic residues in the active center cavity are likely to participate in substrate transport/binding.
+*[[Galactosidase 3D structures|Galactosidase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-PBG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PBG OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis., Wiesmann C, Hengstenberg W, Schulz GE, J Mol Biol. 1997 Jun 27;269(5):851-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9223646 9223646]
-[[Category: 6-phospho-beta-galactosidase]]
 [[Category: Lactococcus lactis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Schulz, G E.]]
+[[Category: Schulz GE]]
-[[Category: Wiesmann, C.]]
+[[Category: Wiesmann C]]
-[[Category: glycosyl hydrolase]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:35:05 2008''