1kum

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1kum" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kum" /> '''GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN...)
Current revision (00:11, 21 November 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1kum.gif|left|200px]]<br /><applet load="1kum" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1kum" />
 
-
'''GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE'''<br />
 
-
==Overview==
+
==GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE==
-
The solution structure of the granular starch binding domain (SBD) of, glucoamylase 1 from Aspergillus niger has been determined by heteronuclear, multidimensional nuclear magnetic resonance spectroscopy and simulated, annealing. A total of 1092 nuclear Overhauser enhancement-derived 1H-1H, distance constraints, 137 dihedral constraints and 86 hydrogen bond, constraints were incorporated into an X-PLOR simulated annealing and, refinement protocol. The family of calculated structures shows a well, defined beta-sheet structure consisting of one parallel and six, antiparallel pairs of beta-strands which forms an open-sided beta-barrel., The root-mean-square deviation (rmsd) of 53 individual structures to the, calculated average structure for the backbone atoms of residues excluding, the N terminus and two mobile loops is 0.57(+/-0.10) A while the rmsd for, backbone atoms in beta-strands is 0.45(+/-0.08) A. Structural features of, the SBD in solution are compared to the X-ray crystal structure of a, homologous domain of cyclodextrin glycosyltransferase (CGTase) in the free, and bound forms. Titration studies with two ligands, maltoheptaose and, beta-cyclodextrin, show the existence of two binding sites. Examination of, the tertiary structures shows these two sites to be at one end of the, molecule on opposite faces. The majority of residues showing the largest, 1H and 15N chemical shift changes are located in loop regions. Many, residues implicated in binding, based on these changes, are similar in, location to previously identified binding site residues in the crystal, structures of CGTase. Overall, the shift changes are small indicating that, the SBD does not undergo large conformational changes upon ligand binding.
+
<StructureSection load='1kum' size='340' side='right'caption='[[1kum]]' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1kum]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KUM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KUM FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 1 model</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=1kum FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kum OCA], [https://pdbe.org/1kum PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kum RCSB], [https://www.ebi.ac.uk/pdbsum/1kum PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kum ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AMYG_ASPNG AMYG_ASPNG]
 +
== 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/ku/1kum_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1kum ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The solution structure of the granular starch binding domain (SBD) of glucoamylase 1 from Aspergillus niger has been determined by heteronuclear multidimensional nuclear magnetic resonance spectroscopy and simulated annealing. A total of 1092 nuclear Overhauser enhancement-derived 1H-1H distance constraints, 137 dihedral constraints and 86 hydrogen bond constraints were incorporated into an X-PLOR simulated annealing and refinement protocol. The family of calculated structures shows a well defined beta-sheet structure consisting of one parallel and six antiparallel pairs of beta-strands which forms an open-sided beta-barrel. The root-mean-square deviation (rmsd) of 53 individual structures to the calculated average structure for the backbone atoms of residues excluding the N terminus and two mobile loops is 0.57(+/-0.10) A while the rmsd for backbone atoms in beta-strands is 0.45(+/-0.08) A. Structural features of the SBD in solution are compared to the X-ray crystal structure of a homologous domain of cyclodextrin glycosyltransferase (CGTase) in the free and bound forms. Titration studies with two ligands, maltoheptaose and beta-cyclodextrin, show the existence of two binding sites. Examination of the tertiary structures shows these two sites to be at one end of the molecule on opposite faces. The majority of residues showing the largest 1H and 15N chemical shift changes are located in loop regions. Many residues implicated in binding, based on these changes, are similar in location to previously identified binding site residues in the crystal structures of CGTase. Overall, the shift changes are small indicating that the SBD does not undergo large conformational changes upon ligand binding.
-
==About this Structure==
+
Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy.,Sorimachi K, Jacks AJ, Le Gal-Coeffet MF, Williamson G, Archer DB, Williamson MP J Mol Biol. 1996 Jun 28;259(5):970-87. PMID:8683599<ref>PMID:8683599</ref>
-
1KUM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Active as [http://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KUM OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy., Sorimachi K, Jacks AJ, Le Gal-Coeffet MF, Williamson G, Archer DB, Williamson MP, J Mol Biol. 1996 Jun 28;259(5):970-87. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8683599 8683599]
+
</div>
-
[[Category: Aspergillus niger]]
+
<div class="pdbe-citations 1kum" style="background-color:#fffaf0;"></div>
-
[[Category: Glucan 1,4-alpha-glucosidase]]
+
-
[[Category: Single protein]]
+
-
[[Category: Archer, D.B.]]
+
-
[[Category: Gal-Coeffet, M.F.Le.]]
+
-
[[Category: Jacks, A.J.]]
+
-
[[Category: Sorimachi, K.]]
+
-
[[Category: Williamson, G.]]
+
-
[[Category: Williamson, M.P.]]
+
-
[[Category: hydrolase]]
+
-
[[Category: starch binding domain]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:53:33 2007''
+
==See Also==
 +
*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Aspergillus niger]]
 +
[[Category: Large Structures]]
 +
[[Category: Archer DB]]
 +
[[Category: Jacks AJ]]
 +
[[Category: Le Gal-Coeffet M-F]]
 +
[[Category: Sorimachi K]]
 +
[[Category: Williamson G]]
 +
[[Category: Williamson MP]]

Current revision

GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE

PDB ID 1kum

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kum"
Personal tools