1glm: Difference between revisions

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New page: left|200px<br /><applet load="1glm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1glm, resolution 2.4Å" /> '''REFINED CRYSTAL STRUC...
 
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[[Image:1glm.gif|left|200px]]<br /><applet load="1glm" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1glm, resolution 2.4&Aring;" />
'''REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100'''<br />


==Overview==
==REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100==
The refined crystal structures of a proteolytic fragment of glucoamylase, from Aspergillus awamori var. X100 have been determined at pH 6 and 4 to a, resolution of 2.2 A and 2.4 A, respectively. The models include the, equivalent of residues 1 to 471 of glucoamylase from Aspergillus niger and, a complete interpretation of the solvent structure. The R-factors of the, pH 6 and 4 structures are 0.14 and 0.12, respectively, with, root-mean-square deviations of 0.014 A and 0.012 A from expected, bondlengths. The enzyme has the general shape of a doughnut. The "hole" of, the doughnut consists of a barrier of hydrophobic residues at the center, which separates two water-filled voids, one of which serves as the active, site. Three clusters of water molecules extend laterally from the active, site. One of the lateral clusters connects the deepest recess of the, active site to the surface of the enzyme. The most significant difference, in the pH 4 and 6 structures is the thermal parameter of water 500, the, putative nucleophile in the hydrolysis of maltooligosaccharides. Water 500, is associated more tightly with the enzyme at pH 4 (the pH of optimum, catalysis) than at pH 6. In contrast to water 500, Glu179, the putative, catalytic acid of glucoamylase, retains the same conformation in both, structures and is in an environment that would favor the ionized, rather, than the acid form of the side-chain. Glycosyl chains of 5 and 8 sugar, residues are linked to Asparagines 171 and 395, respectively. The, conformations of the two glycosyl chains are similar, being superimposable, on each other with a root-mean-square discrepancy of 1.9 A. The N-glycosyl, chains hydrogen bond to the surface of the protein through their terminal, sugars, but otherwise do not interact strongly with the enzyme. The, structures have ten serine/threonine residues, to each of which is linked, a single mannose sugar. The structure of the ten O-glycosylated residues, taken together suggests a well-defined conformation for proteins that have, extensive O-glycosylation of their polypeptide chain.
<StructureSection load='1glm' size='340' side='right'caption='[[1glm]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1glm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GLM 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1glm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1glm OCA], [https://pdbe.org/1glm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1glm RCSB], [https://www.ebi.ac.uk/pdbsum/1glm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1glm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/AMYG_ASPAW AMYG_ASPAW]
== 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/gl/1glm_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=1glm ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1GLM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori] with MAN as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1GLM OCA].
*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
 
*[[Amylase 3D structures|Amylase 3D structures]]
==Reference==
__TOC__
Refined crystal structures of glucoamylase from Aspergillus awamori var. X100., Aleshin AE, Hoffman C, Firsov LM, Honzatko RB, J Mol Biol. 1994 May 13;238(4):575-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8176747 8176747]
</StructureSection>
[[Category: Aspergillus awamori]]
[[Category: Aspergillus awamori]]
[[Category: Glucan 1,4-alpha-glucosidase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Aleshin AE]]
[[Category: Aleshin, A.E.]]
[[Category: Firsov LM]]
[[Category: Firsov, L.M.]]
[[Category: Hoffman C]]
[[Category: Hoffman, C.]]
[[Category: Honzatko RB]]
[[Category: Honzatko, R.B.]]
[[Category: MAN]]
[[Category: hydrolase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:09:19 2007''

Latest revision as of 14:22, 27 March 2024

REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100REFINED CRYSTAL STRUCTURES OF GLUCOAMYLASE FROM ASPERGILLUS AWAMORI VAR. X100

Structural highlights

1glm is a 1 chain structure with sequence from Aspergillus awamori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMYG_ASPAW

Evolutionary Conservation

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

See Also

1glm, resolution 2.40Å

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