1kul

From Proteopedia

(Difference between revisions)

Current revision

GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, 5 STRUCTURES

Structural highlights

1kul is a 1 chain structure with sequence from Aspergillus niger. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 5 models
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMYG_ASPNG

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 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.

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^[1]

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

References

↑ Sorimachi K, Jacks AJ, Le Gal-Coeffet MF, Williamson G, Archer DB, Williamson MP. Solution structure of the granular starch binding domain of glucoamylase from Aspergillus niger by nuclear magnetic resonance spectroscopy. J Mol Biol. 1996 Jun 28;259(5):970-87. PMID:8683599 doi:http://dx.doi.org/10.1006/jmbi.1996.0374

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/1kul"

@@ Line 1: / Line 1: @@
 ==GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, 5 STRUCTURES==
-<StructureSection load='1kul' size='340' side='right'caption='[[1kul]], [[NMR_Ensembles_of_Models | 5 NMR models]]' scene=''>
+<StructureSection load='1kul' size='340' side='right'caption='[[1kul]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1kul]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/A._niger A. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KUL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1kul]] 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=1KUL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KUL FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kum|1kum]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 5 models</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">A. NIGER GLAA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucan_1,4-alpha-glucosidase Glucan 1,4-alpha-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.3 3.2.1.3] </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=1kul FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kul OCA], [https://pdbe.org/1kul PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kul RCSB], [https://www.ebi.ac.uk/pdbsum/1kul PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kul ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYG_ASPNG AMYG_ASPNG]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 14: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ku/1kul_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: A. niger]]
+[[Category: Aspergillus niger]]
-[[Category: Glucan 1,4-alpha-glucosidase]]
 [[Category: Large Structures]]
-[[Category: Archer, D B]]
+[[Category: Archer DB]]
-[[Category: Gal-Coeffet, M F.Le]]
+[[Category: Jacks AJ]]
-[[Category: Jacks, A J]]
+[[Category: Le Gal-Coeffet M-F]]
-[[Category: Sorimachi, K]]
+[[Category: Sorimachi K]]
-[[Category: Williamson, G]]
+[[Category: Williamson G]]
-[[Category: Williamson, M P]]
+[[Category: Williamson MP]]
-[[Category: Hydrolase]]
-[[Category: Starch binding domain]]

1kul

From Proteopedia

Current revision

GLUCOAMYLASE, GRANULAR STARCH-BINDING DOMAIN, NMR, 5 STRUCTURES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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