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1byd

From Proteopedia

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[[Image:1byd.jpg|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS==
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|PDB= 1byd |SIZE=350|CAPTION= <scene name='initialview01'>1byd</scene>, resolution 2.2&Aring;
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<StructureSection load='1byd' size='340' side='right'caption='[[1byd]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DOM:2&#39;-DEOXYMALTOSE'>DOM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1byd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BYD FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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|GENE=
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<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>, <scene name='pdbligand=PRD_900048:2-deoxy-maltose'>PRD_900048</scene>, <scene name='pdbligand=RR7:2-deoxy-beta-D-arabino-hexopyranose'>RR7</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1byd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1byd OCA], [https://pdbe.org/1byd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1byd RCSB], [https://www.ebi.ac.uk/pdbsum/1byd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1byd ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1byd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1byd OCA], [http://www.ebi.ac.uk/pdbsum/1byd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1byd RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/AMYB_SOYBN AMYB_SOYBN]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/1byd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1byd ConSurf].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS'''
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==See Also==
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*[[Amylase 3D structures|Amylase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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The crystal structures of catalytically competent soybean beta-amylase, unliganded and bathed with small substrates (beta-maltose, maltal), were determined at 1.9-2.2-A resolution. Two molecules of beta-maltose substrate bind to the protein in tandem, with some maltotetraose enzymic condensation product sharing the same binding sites. The beta-amylase soaked with maltal shows a similar arrangement of two bound molecules of 2-deoxymaltose, the enzymic hydration product. In each case the nonreducing ends of the saccharide ligands are oriented toward the base of the protein's active site pocket. The catalytic center, located between the bound disaccharides and found deeper in the pocket than where the inhibitor alpha-cyclodextrin binds, is characterized by the presence of oppositely disposed carboxyl groups of two conserved glutamic acid residues. The OE2 carboxyl of Glu 186 is below the plane of the penultimate glucose residue (Glc 2) of bound maltotetraose, 2.6 A from the oxygen atom of that ligand's penultimate alpha-1,4-glucosidic linkage. The OE2 carboxyl of Glu 380 lies above the plane of Glc 2, 2.8 A from the O-1 atom of the more deeply bound beta-maltose. Saccharide binding does not alter the spatial coordinates of these two carboxyl groups or the overall conformation of the 57-kDa protein. However, the saccharide complexes of the active enzyme are associated with a significant (10 A) local conformational change in a peptide segment of a loop (L3) that borders the active site pocket.(ABSTRACT TRUNCATED AT 250 WORDS)
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==About this Structure==
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1BYD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BYD OCA].
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==Reference==
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Crystal structures of soybean beta-amylase reacted with beta-maltose and maltal: active site components and their apparent roles in catalysis., Mikami B, Degano M, Hehre EJ, Sacchettini JC, Biochemistry. 1994 Jun 28;33(25):7779-87. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8011643 8011643]
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[[Category: Beta-amylase]]
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[[Category: Glycine max]]
[[Category: Glycine max]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Degano, M.]]
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[[Category: Degano M]]
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[[Category: Hehre, E J.]]
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[[Category: Hehre EJ]]
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[[Category: Mikami, B.]]
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[[Category: Mikami B]]
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[[Category: Sacchettini, J C.]]
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[[Category: Sacchettini JC]]
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[[Category: hydrolase(o-glycosyl)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:10:49 2008''
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Current revision

CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS

PDB ID 1byd

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