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2d0h

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{{Seed}}
 
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[[Image:2d0h.png|left|200px]]
 
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==Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide==
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The line below this paragraph, containing "STRUCTURE_2d0h", creates the "Structure Box" on the page.
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<StructureSection load='2d0h' size='340' side='right'caption='[[2d0h]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2d0h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0H FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.1&#8491;</td></tr>
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<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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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{{STRUCTURE_2d0h| PDB=2d0h | SCENE= }}
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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=2d0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0h OCA], [https://pdbe.org/2d0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0h RCSB], [https://www.ebi.ac.uk/pdbsum/2d0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0h ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.
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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/d0/2d0h_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=2d0h ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a pullulan model oligosaccharide (P2; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5; [Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed that the (-) subsites of TVAI are responsible for recognizing both starch and pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages, leading to weak interactions between substrates and the enzyme. Domain N of TVAI is a starch-binding domain acting as an anchor in the catalytic reaction of the enzyme. In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain.
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===Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide===
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Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages.,Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S FEBS J. 2005 Dec;272(23):6145-53. PMID:16302977<ref>PMID:16302977</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2d0h" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16302977}}, adds the Publication Abstract to the page
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*[[Amylase 3D structures|Amylase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16302977 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16302977}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2D0H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermoactinomyces_vulgaris Thermoactinomyces vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0H OCA].
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==Reference==
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Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages., Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S, FEBS J. 2005 Dec;272(23):6145-53. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16302977 16302977]
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[[Category: Alpha-amylase]]
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[[Category: Single protein]]
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[[Category: Thermoactinomyces vulgaris]]
[[Category: Thermoactinomyces vulgaris]]
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[[Category: Abe, A.]]
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[[Category: Abe A]]
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[[Category: Kamitori, S.]]
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[[Category: Kamitori S]]
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[[Category: Sakano, Y.]]
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[[Category: Sakano Y]]
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[[Category: Tonozuka, T.]]
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[[Category: Tonozuka T]]
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[[Category: Yoshida, H.]]
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[[Category: Yoshida H]]
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[[Category: Alpha-amylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 15:13:05 2008''
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Current revision

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P2, a pullulan model oligosaccharide

PDB ID 2d0h

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