1fa2: Difference between revisions

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-[[Image:1fa2.gif|left|200px]]<br /><applet load="1fa2" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1fa2, resolution 2.30&Aring;" />
-'''CRYSTAL STRUCTURE OF BETA-AMYLASE FROM SWEET POTATO'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF BETA-AMYLASE FROM SWEET POTATO==
-Sweet potato beta-amylase is a tetramer of identical subunits, which are, arranged to exhibit 222 molecular symmetry. Its subunit consists of 498, amino acid residues (Mr 55,880). It has been crystallized at room, temperature using polyethylene glycol 1500 as precipitant. The crystals, growing to dimensions of 0.4 mm x 0.4 mm x 1.0 mm within 2 weeks, belong, to the tetragonal space group P4(2)2(1)2 with unit cell dimensions of a =, b = 129.63 A and c = 68.42 A. The asymmetric unit contains 1 subunit of, beta-amylase, with a crystal volume per protein mass (VM) of 2.57 A3/Da, and a solvent content of 52% by volume. The three-dimensional structure of, the tetrameric beta-amylase from sweet potato has been determined by, molecular replacement methods using the monomeric structure of soybean, enzyme as the starting model. The refined subunit model contains 3,863, nonhydrogen protein atoms (488 amino acid residues) and 319 water oxygen, atoms. The current R-value is 20.3% for data in the resolution range of, 8-2.3 A (with 2 sigma cut-off) with good stereochemistry. The subunit, structure of sweet potato beta-amylase (crystallized in the absence of, alpha-cyclodextrin) is very similar to that of soybean beta-amylase, (complexed with alpha-cyclodextrin). The root-mean-square (RMS) difference, for 487 equivalent C alpha atoms of the two beta-amylases is 0.96 A. Each, subunit of sweet potato beta-amylase is composed of a large (alpha/beta)8, core domain, a small one made up of three long loops [L3 (residues, 91-150), L4 (residues 183-258), and L5 (residues 300-327)], and a long, C-terminal loop formed by residues 445-493. Conserved Glu 187, believed to, play an important role in catalysis, is located at the cleft between the, (alpha/beta)8 barrel core and a small domain made up of three long loops, (L3, L4, and L5). Conserved Cys 96, important in the inactivation of, enzyme activity by sulfhydryl reagents, is located at the entrance of the, (alpha/beta)8 barrel.
+<StructureSection load='1fa2' size='340' side='right'caption='[[1fa2]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1fa2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FA2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FA2 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]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900048:2-deoxy-maltose'>PRD_900048</scene>, <scene name='pdbligand=RR7:2-deoxy-beta-D-arabino-hexopyranose'>RR7</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=1fa2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fa2 OCA], [https://pdbe.org/1fa2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fa2 RCSB], [https://www.ebi.ac.uk/pdbsum/1fa2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fa2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYB_IPOBA AMYB_IPOBA]
+== 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/fa/1fa2_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=1fa2 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-FA2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ipomoea_batatas Ipomoea batatas] with DOM and DTT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Beta-amylase Beta-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.2 3.2.1.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FA2 OCA].
+*[[Amylase 3D structures|Amylase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato., Cheong CG, Eom SH, Chang C, Shin DH, Song HK, Min K, Moon JH, Kim KK, Hwang KY, Suh SW, Proteins. 1995 Feb;21(2):105-17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7777485 7777485]
-[[Category: Beta-amylase]]
 [[Category: Ipomoea batatas]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Cheong, C.G.]]
+[[Category: Cheong CG]]
-[[Category: Lee, B.I.]]
+[[Category: Lee BI]]
-[[Category: Suh, S.W.]]
+[[Category: Suh SW]]
-[[Category: DOM]]
-[[Category: DTT]]
-[[Category: tim barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:45:11 2007''