1wdp

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[[Image:1wdp.gif|left|200px]]
 
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{{Structure
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==The role of an inner loop in the catalytic mechanism of soybean beta-amylase==
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|PDB= 1wdp |SIZE=350|CAPTION= <scene name='initialview01'>1wdp</scene>, resolution 1.27&Aring;
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<StructureSection load='1wdp' size='340' side='right'caption='[[1wdp]], [[Resolution|resolution]] 1.27&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1wdp]] 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=1WDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WDP 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]] 1.27&#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=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=1wdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wdp OCA], [https://pdbe.org/1wdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wdp RCSB], [https://www.ebi.ac.uk/pdbsum/1wdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wdp ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1q6c|1Q6C]], [[1byb|1BYB]], [[1bfn|1BFN]], [[1byd|1BYD]], [[1v3h|1V3H]], [[1v3i|1V3I]], [[1wdq|1WDQ]], [[1wdr|1WDR]], [[1wds|1WDS]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wdp OCA], [http://www.ebi.ac.uk/pdbsum/1wdp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wdp 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/wd/1wdp_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=1wdp ConSurf].
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<div style="clear:both"></div>
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'''The role of an inner loop in the catalytic mechanism of soybean beta-amylase'''
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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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Two different conformations of the inner loop (residues 340-346) have been found in the soybean beta-amylase structures. In the "product form", the Thr 342 residue creates hydrogen bonds with Glu 186 (catalytic acid) and with the glucose residues at subsites -1 and +1, whereas most of those interactions are lost in the "apo form". To elucidate the relationship between the structural states of the inner loop and the catalytic mechanism, Thr 342 was mutated to Val, Ser, and Ala, respectively, and their crystal structures complexed with maltose were determined together with that of the apo enzyme at 1.27-1.64 A resolutions. The k(cat) values of the T342V, T342S, and T342A mutants decreased by 13-, 360-, and 1700-fold, respectively, compared to that of the wild-type enzyme. Whereas the inner loops in the wild-type/maltose and T342V/maltose complexes adopted the product form, those of the T342S/maltose and T342A/maltose complexes showed the apo form. Structural analyses suggested that the side chain of Thr 342 in product form plays an important role in distorting the sugar ring at subsite -1, stabilizing the deprotonated form of Glu 186, and grasping the glucose residue of the remaining substrate at subsite +1. The third hypothesis was proved by the fact that T342V hydrolyzes maltoheptaose following only multichain attack in contrast to multiple attack of the wild-type enzyme.
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==About this Structure==
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1WDP 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=1WDP OCA].
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==Reference==
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Structural analysis of threonine 342 mutants of soybean beta-amylase: role of a conformational change of the inner loop in the catalytic mechanism., Kang YN, Tanabe A, Adachi M, Utsumi S, Mikami B, Biochemistry. 2005 Apr 5;44(13):5106-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15794648 15794648]
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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: Adachi, M.]]
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[[Category: Adachi M]]
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[[Category: Kang, Y N.]]
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[[Category: Kang YN]]
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[[Category: Mikami, B.]]
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[[Category: Mikami B]]
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[[Category: Utsumi, S.]]
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[[Category: Utsumi S]]
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[[Category: (beta/alpha)8 barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:34:49 2008''
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Current revision

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

PDB ID 1wdp

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