2d0g: Difference between revisions

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<StructureSection load='2d0g' size='340' side='right'caption='[[2d0g]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='2d0g' size='340' side='right'caption='[[2d0g]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2d0g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0G FirstGlance]. <br>
<table><tr><td colspan='2'>[[2d0g]] 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=2D0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D0G FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ji1|1ji1]], [[2d0f|2d0f]], [[2d0h|2d0h]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <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>, <scene name='pdbligand=PRD_900005:beta-cellobiose'>PRD_900005</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] </span></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=2d0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0g OCA], [https://pdbe.org/2d0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0g RCSB], [https://www.ebi.ac.uk/pdbsum/2d0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0g ProSAT]</span></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=2d0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0g OCA], [https://pdbe.org/2d0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d0g RCSB], [https://www.ebi.ac.uk/pdbsum/2d0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d0g ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU]] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.  
[https://www.uniprot.org/uniprot/NEPU1_THEVU NEPU1_THEVU] Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Alpha-amylase]]
[[Category: Atcc 43649]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Abe, A]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Kamitori, S]]
[[Category: Abe A]]
[[Category: Sakano, Y]]
[[Category: Kamitori S]]
[[Category: Tonozuka, T]]
[[Category: Sakano Y]]
[[Category: Yoshida, H]]
[[Category: Tonozuka T]]
[[Category: Hydrolase]]
[[Category: Yoshida H]]

Latest revision as of 14:33, 22 May 2024

Crystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P5, a pullulan model oligosaccharideCrystal Structure of Thermoactinomyces vulgaris R-47 Alpha-Amylase 1 (TVAI) Mutant D356N/E396Q complexed with P5, a pullulan model oligosaccharide

Structural highlights

2d0g is a 1 chain structure with sequence from Thermoactinomyces vulgaris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NEPU1_THEVU Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Also hydrolyzes cyclodextrins.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Abe A, Yoshida H, Tonozuka T, Sakano Y, Kamitori S. 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. FEBS J. 2005 Dec;272(23):6145-53. PMID:16302977 doi:http://dx.doi.org/10.1111/j.1742-4658.2005.05013.x

2d0g, resolution 2.60Å

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