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==Crystal Structure Analysis of Thermoactinomyces vulgaris R-47 alpha-Amylase 1==
==Crystal Structure Analysis of Thermoactinomyces vulgaris R-47 alpha-Amylase 1==
<StructureSection load='1ji1' size='340' side='right' caption='[[1ji1]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='1ji1' size='340' side='right'caption='[[1ji1]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ji1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43649 Atcc 43649]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JI1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ji1]] is a 2 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=1JI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JI1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.6&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ji2|1ji2]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://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=1ji1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji1 OCA], [https://pdbe.org/1ji1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ji1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ji1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji1 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ji1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji1 OCA], [http://pdbe.org/1ji1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji1 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji1 PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1ji1_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ji/1ji1_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 20: Line 20:
</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=1ji1 ConSurf].
</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=1ji1 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystal structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) and alpha-amylase 2 (TVAII) have been determined at 1.6 A and 2.3 A resolution, respectively. The structures of TVAI and TVAII have been refined, R-factor of 0.182 (R(free)=0.206) and 0.179 (0.224), respectively, with good chemical geometries. Both TVAI and TVAII have four domains, N, A, B and C, and all very similar in structure. However, there are some differences in the structures between them. Domain N of TVAI interacts strongly with domains A and B, giving a spherical shape structure to the enzyme, while domain N of TVAII is isolated from the other domains, which leads to the formation of a dimer. TVAI has three bound Ca ions, whereas TVAII has only one. TVAI has eight extra loops compared to TVAII, while TVAII has two extra loops compared to TVAI. TVAI can hydrolyze substrates more efficiently than TVAII with a high molecular mass such as starch, while TVAII is much more active against cyclodextrins than TVAI and other alpha-amylases. A structural comparison of the active sites has clearly revealed this difference in substrate specificity.
Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution.,Kamitori S, Abe A, Ohtaki A, Kaji A, Tonozuka T, Sakano Y J Mol Biol. 2002 Apr 26;318(2):443-53. PMID:12051850<ref>PMID:12051850</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ji1" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Amylase|Amylase]]
*[[Amylase 3D structures|Amylase 3D structures]]
*[[User:Gabriel Pons/Sandbox 2|User:Gabriel Pons/Sandbox 2]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Alpha-amylase]]
[[Category: Large Structures]]
[[Category: Atcc 43649]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Abe, A]]
[[Category: Abe A]]
[[Category: Kaji, A]]
[[Category: Kaji A]]
[[Category: Kamitori, S]]
[[Category: Kamitori S]]
[[Category: Ohtaki, A]]
[[Category: Ohtaki A]]
[[Category: Sakano, Y]]
[[Category: Sakano Y]]
[[Category: Tonozuka, T]]
[[Category: Tonozuka T]]
[[Category: Beta/alpha barrel]]
[[Category: Hydrolase]]

Latest revision as of 16:24, 13 March 2024

Crystal Structure Analysis of Thermoactinomyces vulgaris R-47 alpha-Amylase 1Crystal Structure Analysis of Thermoactinomyces vulgaris R-47 alpha-Amylase 1

Structural highlights

1ji1 is a 2 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 1.6Å
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.

See Also

1ji1, resolution 1.60Å

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