1j0k: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1j0k.jpg|left|200px]]<br /><applet load="1j0k" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1j0k, resolution 3.2&Aring;" />
-'''Crystal structure of neopullulanase E357Q complex with isopanose'''<br />
-==Overview==
+==Crystal structure of neopullulanase E357Q complex with isopanose==
-Crystal structures of Bacillus stearothermophilus TRS40 neopullulanase and, its complexes with panose, maltotetraose and isopanose were determined at, resolutions of 1.9, 2.4, 2.8 and 3.2A, respectively. Since the latter two, carbohydrates are substrates of this enzyme, a deactivated mutant at the, catalytic residue Glu357--&gt;Gln was used for complex crystallization. The, structures were refined at accuracies with r.m.s. deviations of bond, lengths and bond angles ranging from 0.005A to 0.008A and 1.3 degrees to, 1.4 degrees, respectively. The active enzyme forms a dimer in the, crystalline state and in solution. The monomer enzyme is composed of four, domains, N, A, B and C, and has a (beta/alpha)(8)-barrel in domain A. The, active site lies between domain A and domain N from the other monomer. The, results show that dimer formation makes the active-site cleft narrower, than those of ordinary alpha-amylases, which may contribute to the unique, substrate specificity of this enzyme toward both alpha-1,4 and, alpha-1,6-glucosidic linkages. This specificity may be influenced by the, subsite structure. Only subsites -1 and -2 are commonly occupied by the, product and substrates, suggesting that equivocal recognition occurs at, the other subsites, which contributes to the wide substrate specificity of, this enzyme.
+<StructureSection load='1j0k' size='340' side='right'caption='[[1j0k]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1j0k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J0K 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]] 3.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=1j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0k OCA], [https://pdbe.org/1j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j0k RCSB], [https://www.ebi.ac.uk/pdbsum/1j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NEPU_GEOSE NEPU_GEOSE] Hydrolyzes pullulan efficiently but only a small amount of starch. Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Cleaves also (1-6)-alpha-glucosidic linkages to form maltotriose.
+== 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/j0/1j0k_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=1j0k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of Bacillus stearothermophilus TRS40 neopullulanase and its complexes with panose, maltotetraose and isopanose were determined at resolutions of 1.9, 2.4, 2.8 and 3.2A, respectively. Since the latter two carbohydrates are substrates of this enzyme, a deactivated mutant at the catalytic residue Glu357--&gt;Gln was used for complex crystallization. The structures were refined at accuracies with r.m.s. deviations of bond lengths and bond angles ranging from 0.005A to 0.008A and 1.3 degrees to 1.4 degrees, respectively. The active enzyme forms a dimer in the crystalline state and in solution. The monomer enzyme is composed of four domains, N, A, B and C, and has a (beta/alpha)(8)-barrel in domain A. The active site lies between domain A and domain N from the other monomer. The results show that dimer formation makes the active-site cleft narrower than those of ordinary alpha-amylases, which may contribute to the unique substrate specificity of this enzyme toward both alpha-1,4 and alpha-1,6-glucosidic linkages. This specificity may be influenced by the subsite structure. Only subsites -1 and -2 are commonly occupied by the product and substrates, suggesting that equivocal recognition occurs at the other subsites, which contributes to the wide substrate specificity of this enzyme.
-==About this Structure==
+Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase.,Hondoh H, Kuriki T, Matsuura Y J Mol Biol. 2003 Feb 7;326(1):177-88. PMID:12547200<ref>PMID:12547200</ref>
-J0K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Active as [http://en.wikipedia.org/wiki/Neopullulanase Neopullulanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.135 3.2.1.135] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J0K OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase., Hondoh H, Kuriki T, Matsuura Y, J Mol Biol. 2003 Feb 7;326(1):177-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12547200 12547200]
+</div>
+<div class="pdbe-citations 1j0k" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Neopullulanase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Hondoh H]]
-[[Category: Hondoh, H.]]
+[[Category: Kuriki T]]
-[[Category: Kuriki, T.]]
+[[Category: Matsuura Y]]
-[[Category: Matsuura, Y.]]
-[[Category: beta-alpha-barrels]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:50:07 2007''