1ud4: Difference between revisions

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[[Image:1ud4.jpg|left|200px]]


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==Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)==
The line below this paragraph, containing "STRUCTURE_1ud4", creates the "Structure Box" on the page.
<StructureSection load='1ud4' size='340' side='right'caption='[[1ud4]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1ud4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._KSM-K38 Bacillus sp. KSM-K38]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UD4 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1ud4|  PDB=1ud4 |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ud4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ud4 OCA], [https://pdbe.org/1ud4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ud4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ud4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ud4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q93I48_9BACI Q93I48_9BACI]
== 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/ud/1ud4_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=1ud4 ConSurf].
<div style="clear:both"></div>


'''Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)'''
==See Also==
 
*[[Amylase 3D structures|Amylase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.
[[Category: Bacillus sp. KSM-K38]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Fujihashi M]]
1UD4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UD4 OCA].
[[Category: Hagihara H]]
 
[[Category: Ito S]]
==Reference==
[[Category: Kita A]]
Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites., Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K, J Biol Chem. 2003 Jul 4;278(27):24818-24. Epub 2003 Apr 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12719434 12719434]
[[Category: Miki K]]
[[Category: Alpha-amylase]]
[[Category: Nonaka T]]
[[Category: Bacteria]]
[[Category: Ozaki K]]
[[Category: Single protein]]
[[Category: Fujihashi, M.]]
[[Category: Hagihara, H.]]
[[Category: Ito, S.]]
[[Category: Kita, A.]]
[[Category: Miki, K.]]
[[Category: Nonaka, T.]]
[[Category: Ozaki, K.]]
[[Category: Alkaline]]
[[Category: Alpha-amylase]]
[[Category: Calcium-free]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:03:34 2008''

Latest revision as of 09:16, 3 April 2024

Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)

Structural highlights

1ud4 is a 1 chain structure with sequence from Bacillus sp. KSM-K38. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.15Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q93I48_9BACI

Evolutionary Conservation

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

See Also

1ud4, resolution 2.15Å

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