1ud3

From Proteopedia

(Difference between revisions)

Revision as of 23:51, 27 December 2023

Crystal structure of AmyK38 N289H mutant

Structural highlights

1ud3 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.

Publication Abstract from PubMed

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.

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:12719434^[1]

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

References

↑ Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K. Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites. J Biol Chem. 2003 Jul 4;278(27):24818-24. Epub 2003 Apr 28. PMID:12719434 doi:10.1074/jbc.M212763200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ud3"

@@ Line 3: / Line 3: @@
 <StructureSection load='1ud3' size='340' side='right'caption='[[1ud3]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ud3]] 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=1UD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UD3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ud3]] 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=1UD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UD3 FirstGlance]. <br>
-</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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ud2|1ud2]], [[1ud4|1ud4]], [[1ud5|1ud5]], [[1ud6|1ud6]], [[1ud8|1ud8]]</div></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='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=1ud3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ud3 OCA], [https://pdbe.org/1ud3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ud3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ud3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ud3 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93I48_9BACI Q93I48_9BACI]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Alpha-amylase]]
+[[Category: Bacillus sp. KSM-K38]]
-[[Category: Bacillus sp. ksm-k38]]
 [[Category: Large Structures]]
-[[Category: Fujihashi, M]]
+[[Category: Fujihashi M]]
-[[Category: Hagihara, H]]
+[[Category: Hagihara H]]
-[[Category: Ito, S]]
+[[Category: Ito S]]
-[[Category: Kita, A]]
+[[Category: Kita A]]
-[[Category: Miki, K]]
+[[Category: Miki K]]
-[[Category: Nonaka, T]]
+[[Category: Nonaka T]]
-[[Category: Ozaki, K]]
+[[Category: Ozaki K]]
-[[Category: Alkaline]]
-[[Category: Calcium-free]]
-[[Category: Hydrolase]]

1ud3

From Proteopedia

Revision as of 23:51, 27 December 2023

Crystal structure of AmyK38 N289H mutant

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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