1ud4: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1ud4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ud4, resolution 2.15Å" /> '''Crystal structure of...
 
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ud4.jpg|left|200px]]<br /><applet load="1ud4" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ud4, resolution 2.15&Aring;" />
'''Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)'''<br />


==Overview==
==Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)==
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.
<StructureSection load='1ud4' size='340' side='right'caption='[[1ud4]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>


==About this Structure==
==See Also==
1UD4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._ksm-k38 Bacillus sp. ksm-k38] with NA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UD4 OCA].
*[[Amylase 3D structures|Amylase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12719434 12719434]
[[Category: Bacillus sp. KSM-K38]]
[[Category: Alpha-amylase]]
[[Category: Large Structures]]
[[Category: Bacillus sp. ksm-k38]]
[[Category: Fujihashi M]]
[[Category: Single protein]]
[[Category: Hagihara H]]
[[Category: Fujihashi, M.]]
[[Category: Ito S]]
[[Category: Hagihara, H.]]
[[Category: Kita A]]
[[Category: Ito, S.]]
[[Category: Miki K]]
[[Category: Kita, A.]]
[[Category: Nonaka T]]
[[Category: Miki, K.]]
[[Category: Ozaki K]]
[[Category: Nonaka, T.]]
[[Category: Ozaki, K.]]
[[Category: NA]]
[[Category: alkaline]]
[[Category: alpha-amylase]]
[[Category: calcium-free]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:46:59 2007''

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

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1ud4&oldid=4118285"