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[[Image:1vb9.gif|left|200px]]


{{Structure
==Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product==
|PDB= 1vb9 |SIZE=350|CAPTION= <scene name='initialview01'>1vb9</scene>, resolution 2.20&Aring;
<StructureSection load='1vb9' size='340' side='right'caption='[[1vb9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:GLUCOSE'>GLC</scene>
<table><tr><td colspan='2'>[[1vb9]] 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=1VB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VB9 FirstGlance]. <br>
|ACTIVITY= <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='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>
|GENE=
<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></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vb9 OCA], [https://pdbe.org/1vb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vb9 RCSB], [https://www.ebi.ac.uk/pdbsum/1vb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vb9 ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vb9 OCA], [http://www.ebi.ac.uk/pdbsum/1vb9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1vb9 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/NEPU2_THEVU NEPU2_THEVU] Hydrolyzes pullulan efficiently but only a small amount of starch. Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Cleaves also (1-6)-alpha-glucosidic linkages to form maltotriose.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vb/1vb9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1vb9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Alphan alpha-amylase (TVA II) from Thermoactinomyces vulgaris R-47 efficiently hydrolyzes alpha-1,4-glucosidic linkages of pullulan to produce panose in addition to hydrolyzing starch. TVA II also hydrolyzes alpha-1,4-glucosidic linkages of cyclodextrins and alpha-1,6-glucosidic linkages of isopanose. To clarify the basis for this wide substrate specificity of TVA II, we soaked 4(3)-alpha-panosylpanose (4(3)-P2) (a pullulan hydrolysate composed of two panosyl units) into crystals of D325N inactive mutated TVA II. We then determined the crystal structure of TVA II complexed with 4(2)-alpha-panosylpanose (4(2)-P2), which was produced by transglycosylation from 4(3)-P2, at 2.2-A resolution. The shape of the active cleft of TVA II is unique among those of alpha-amylase family enzymes due to a loop (residues 193-218) that is located at the end of the cleft around the nonreducing region and forms a 'dam'-like bank. Because this loop is short in TVA II, the active cleft is wide and shallow around the nonreducing region. It is assumed that this short loop is one of the reasons for the wide substrate specificity of TVA II. While Trp356 is involved in the binding of Glc +2 of the substrate, it appears that Tyr374 in proximity to Trp356 plays two roles: one is fixing the orientation of Trp356 in the substrate-liganded state and the other is supplying the water that is necessary for substrate hydrolysis.


'''Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product'''
The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product.,Mizuno M, Tonozuka T, Uechi A, Ohtaki A, Ichikawa K, Kamitori S, Nishikawa A, Sakano Y Eur J Biochem. 2004 Jun;271(12):2530-8. PMID:15182368<ref>PMID:15182368</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1vb9" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Alphan alpha-amylase (TVA II) from Thermoactinomyces vulgaris R-47 efficiently hydrolyzes alpha-1,4-glucosidic linkages of pullulan to produce panose in addition to hydrolyzing starch. TVA II also hydrolyzes alpha-1,4-glucosidic linkages of cyclodextrins and alpha-1,6-glucosidic linkages of isopanose. To clarify the basis for this wide substrate specificity of TVA II, we soaked 4(3)-alpha-panosylpanose (4(3)-P2) (a pullulan hydrolysate composed of two panosyl units) into crystals of D325N inactive mutated TVA II. We then determined the crystal structure of TVA II complexed with 4(2)-alpha-panosylpanose (4(2)-P2), which was produced by transglycosylation from 4(3)-P2, at 2.2-A resolution. The shape of the active cleft of TVA II is unique among those of alpha-amylase family enzymes due to a loop (residues 193-218) that is located at the end of the cleft around the nonreducing region and forms a 'dam'-like bank. Because this loop is short in TVA II, the active cleft is wide and shallow around the nonreducing region. It is assumed that this short loop is one of the reasons for the wide substrate specificity of TVA II. While Trp356 is involved in the binding of Glc +2 of the substrate, it appears that Tyr374 in proximity to Trp356 plays two roles: one is fixing the orientation of Trp356 in the substrate-liganded state and the other is supplying the water that is necessary for substrate hydrolysis.
*[[Amylase 3D structures|Amylase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1VB9 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=1VB9 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product., Mizuno M, Tonozuka T, Uechi A, Ohtaki A, Ichikawa K, Kamitori S, Nishikawa A, Sakano Y, Eur J Biochem. 2004 Jun;271(12):2530-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15182368 15182368]
[[Category: Alpha-amylase]]
[[Category: Single protein]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Thermoactinomyces vulgaris]]
[[Category: Ichikawa, K.]]
[[Category: Ichikawa K]]
[[Category: Kamitori, S.]]
[[Category: Kamitori S]]
[[Category: Mizuno, M.]]
[[Category: Mizuno M]]
[[Category: Nishikawa, A.]]
[[Category: Nishikawa A]]
[[Category: Ohtaki, A.]]
[[Category: Ohtaki A]]
[[Category: Sakano, Y.]]
[[Category: Sakano Y]]
[[Category: Tonozuka, T.]]
[[Category: Tonozuka T]]
[[Category: Uechi, A.]]
[[Category: Uechi A]]
[[Category: (beta/alpha)8 barrel]]
[[Category: gh family 13]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:21:58 2008''

Latest revision as of 10:51, 25 October 2023

Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated productCrystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product

Structural highlights

1vb9 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 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NEPU2_THEVU Hydrolyzes pullulan efficiently but only a small amount of starch. Endohydrolysis of 1,4-alpha-glucosidic linkages in pullulan to form panose. Cleaves also (1-6)-alpha-glucosidic linkages to form maltotriose.

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

Alphan alpha-amylase (TVA II) from Thermoactinomyces vulgaris R-47 efficiently hydrolyzes alpha-1,4-glucosidic linkages of pullulan to produce panose in addition to hydrolyzing starch. TVA II also hydrolyzes alpha-1,4-glucosidic linkages of cyclodextrins and alpha-1,6-glucosidic linkages of isopanose. To clarify the basis for this wide substrate specificity of TVA II, we soaked 4(3)-alpha-panosylpanose (4(3)-P2) (a pullulan hydrolysate composed of two panosyl units) into crystals of D325N inactive mutated TVA II. We then determined the crystal structure of TVA II complexed with 4(2)-alpha-panosylpanose (4(2)-P2), which was produced by transglycosylation from 4(3)-P2, at 2.2-A resolution. The shape of the active cleft of TVA II is unique among those of alpha-amylase family enzymes due to a loop (residues 193-218) that is located at the end of the cleft around the nonreducing region and forms a 'dam'-like bank. Because this loop is short in TVA II, the active cleft is wide and shallow around the nonreducing region. It is assumed that this short loop is one of the reasons for the wide substrate specificity of TVA II. While Trp356 is involved in the binding of Glc +2 of the substrate, it appears that Tyr374 in proximity to Trp356 plays two roles: one is fixing the orientation of Trp356 in the substrate-liganded state and the other is supplying the water that is necessary for substrate hydrolysis.

The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product.,Mizuno M, Tonozuka T, Uechi A, Ohtaki A, Ichikawa K, Kamitori S, Nishikawa A, Sakano Y Eur J Biochem. 2004 Jun;271(12):2530-8. PMID:15182368[1]

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

See Also

References

  1. ↑ Mizuno M, Tonozuka T, Uechi A, Ohtaki A, Ichikawa K, Kamitori S, Nishikawa A, Sakano Y. The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product. Eur J Biochem. 2004 Jun;271(12):2530-8. PMID:15182368 doi:10.1111/j.1432-1033.2004.04183.x

1vb9, resolution 2.20Å

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