1j11: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1j11.png|left|200px]]
-{{STRUCTURE_1j11|  PDB=1j11  |  SCENE=  }}
+==beta-amylase from Bacillus cereus var. mycoides in complex with alpha-EPG==
+<StructureSection load='1j11' size='340' side='right'caption='[[1j11]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1j11]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J11 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]] 2&#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=EPG:2-HYDROXYMETHYL-6-OXIRANYLMETHOXY-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>EPG</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=1j11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j11 OCA], [https://pdbe.org/1j11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j11 RCSB], [https://www.ebi.ac.uk/pdbsum/1j11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j11 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYB_BACCE AMYB_BACCE]
+== 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/j1/1j11_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1j11 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of beta-amylase from Bacillus cereus var. mycoides in complexes with five inhibitors were solved. The inhibitors used were three substrate analogs, i.e. glucose, maltose (product), and a synthesized compound, O-alpha-D-glucopyranosyl-(1--&gt;4)-O-alpha-D-glucopyranosyl-(1--&gt;4)-D-xylopy ranose (GGX), and two affinity-labeling reagents with an epoxy alkyl group at the reducing end of glucose. For all inhibitors, one molecule was bound at the active site cleft and the non-reducing end glucose of the four inhibitors except GGX was located at subsite 1, accompanied by a large conformational change of the flexible loop (residues 93-97), which covered the bound inhibitor. In addition, another molecule of maltose or GGX was bound about 30 A away from the active site. A large movement of residues 330 and 331 around subsite 3 was also observed upon the binding of GGX at subsites 3 to 5. Two affinity-labeling reagents, alpha-EPG and alpha-EBG, were covalently bound to a catalytic residue (Glu-172). A substrate recognition mechanism for the beta-amylase was discussed based on the modes of binding of these inhibitors in the active site cleft.
-===beta-amylase from Bacillus cereus var. mycoides in complex with alpha-EPG===
+Crystal structures of beta-amylase from Bacillus cereus var mycoides in complexes with substrate analogs and affinity-labeling reagents.,Oyama T, Miyake H, Kusunoki M, Nitta Y J Biochem. 2003 Apr;133(4):467-74. PMID:12761294<ref>PMID:12761294</ref>
-{{ABSTRACT_PUBMED_12761294}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1j11" style="background-color:#fffaf0;"></div>
-[[1j11]] is a 4 chain structure of [[Alpha-Amylase]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus Bacillus cereus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J11 OCA].
 ==See Also==
-*[[Alpha-Amylase|Alpha-Amylase]]
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:012761294</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus cereus]]
-[[Category: Beta-amylase]]
+[[Category: Large Structures]]
-[[Category: Kusunoki, M.]]
+[[Category: Kusunoki M]]
-[[Category: Miyake, H.]]
+[[Category: Miyake H]]
-[[Category: Nitta, Y.]]
+[[Category: Nitta Y]]
-[[Category: Oyama, T.]]
+[[Category: Oyama T]]
-[[Category: Beta-amylase]]
-[[Category: Hydrolase]]
-[[Category: Raw-starch binding domain]]