1e3x: Difference between revisions

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-[[Image:1e3x.png|left|200px]]
-{{STRUCTURE_1e3x|  PDB=1e3x  |  SCENE=  }}
+==Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.92A==
+<StructureSection load='1e3x' size='340' side='right'caption='[[1e3x]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1e3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E3X FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=1e3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e3x OCA], [https://pdbe.org/1e3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e3x RCSB], [https://www.ebi.ac.uk/pdbsum/1e3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e3x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMY_BACAM AMY_BACAM]
+== 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/e3/1e3x_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=1e3x ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Several chimeric alpha-amylases genes were constructed by an in vivo recombination technique from the Bacillus amyloliquefaciens and Bacillus licheniformis genes. One of the fusion amylases (hereafter BA2), consisting of residues 1-300 from B. amyloliquefaciens and 301-483 from B. licheniformis, has been extensively studied by X-ray crystallography at resolutions between 2.2 and 1.7 A. The 3-dimensional structure of the native enzyme was solved by multiple isomorphous replacement, and refined at a resolution of 1.7 A. It consists of 483 amino acids, organized similarly to the known B. lichiniformis alpha-amylase structure [Machius et al. (1995) J. Mol. Biol. 246, 545-559], but features 4 bound calcium ions. Two of these form part of a linear cluster of three ions, the central ion being attributed to sodium. This cluster lies at the junction of the A and B domains with one calcium of the cluster structurally equivalent to the major Ca(2+) binding site of fungal alpha-amylases. The third calcium ion is found at the interface of the A and C domains. BA2 contains a fourth calcium site, not observed in the B. licheniformis alpha-amylase structure. It is found on the C domain where it bridges the two beta-sheets. Three acid residues (Glu261, Asp328, and Asp231) form an active site similar to that seen in other amylases. In the presence of TRIS buffer, a single molecule of TRIS occupies the -1 subsite of the enzyme where it is coordinated by the three active-center carboxylates. Kinetic data reveal that BA2 displays properties intermediate to those of its parents. Data for crystals soaked in maltooligosaccharides reveal the presence of a maltotriose binding site on the N-terminal face of the (beta/alpha)(8) barrel of the molecule, not previously described for any alpha-amylase structure, the biological function of which is unclear. Data for a complex soaked with the tetrasaccharide inhibitor acarbose, at 1.9 A, reveal a decasaccharide moiety, spanning the -7 to +3 subsites of the enzyme. The unambiguous presence of three unsaturated rings in the (2)H(3) half-chair/(2)E envelope conformation, adjacent to three 6-deoxypyranose units, clearly demonstrates synthesis of this acarbose-derived decasaccharide by a two-step transglycosylation mechanism.
-===NATIVE STRUCTURE OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND B. LICHENIFORMIS AT 1.92A===
+Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.,Brzozowski AM, Lawson DM, Turkenburg JP, Bisgaard-Frantzen H, Svendsen A, Borchert TV, Dauter Z, Wilson KS, Davies GJ Biochemistry. 2000 Aug 8;39(31):9099-107. PMID:10924103<ref>PMID:10924103</ref>
-{{ABSTRACT_PUBMED_10924103}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1e3x" style="background-color:#fffaf0;"></div>
-[[1e3x]] is a 1 chain structure of [[Alpha-Amylase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_amyloliquefaciens Bacillus amyloliquefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3X OCA].
 ==See Also==
-*[[Alpha-Amylase|Alpha-Amylase]]
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010924103</ref><references group="xtra"/>
+__TOC__
-[[Category: Alpha-amylase]]
+</StructureSection>
 [[Category: Bacillus amyloliquefaciens]]
-[[Category: Bisgaard-Frantzen, H.]]
+[[Category: Large Structures]]
-[[Category: Borchert, T V.]]
+[[Category: Bisgaard-Frantzen H]]
-[[Category: Brzozowski, A M.]]
+[[Category: Borchert TV]]
-[[Category: Dauter, Z.]]
+[[Category: Brzozowski AM]]
-[[Category: Davies, G J.]]
+[[Category: Dauter Z]]
-[[Category: Lawson, D M.]]
+[[Category: Davies GJ]]
-[[Category: Svendsen, A.]]
+[[Category: Lawson DM]]
-[[Category: Turkenburg, J P.]]
+[[Category: Svendsen A]]
-[[Category: Wilson, K S.]]
+[[Category: Turkenburg JP]]
-[[Category: Amylase]]
+[[Category: Wilson KS]]
-[[Category: Family 13]]
-[[Category: Hydrolase]]