1e7m: Difference between revisions

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<StructureSection load='1e7m' size='340' side='right'caption='[[1e7m]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
<StructureSection load='1e7m' size='340' side='right'caption='[[1e7m]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1e7m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"ascococcus_mesenteroides"_tsenkovskii_1878 "ascococcus mesenteroides" tsenkovskii 1878]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E7M FirstGlance]. <br>
<table><tr><td colspan='2'>[[1e7m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Leuconostoc_mesenteroides Leuconostoc mesenteroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E7M FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.54&#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;'>[[1dpg|1dpg]], [[1e77|1e77]], [[2dpg|2dpg]], [[1e7y|1e7y]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PLMZ/D177N ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1245 "Ascococcus mesenteroides" Tsenkovskii 1878])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase Glucose-6-phosphate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.49 1.1.1.49] </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=1e7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7m OCA], [https://pdbe.org/1e7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e7m RCSB], [https://www.ebi.ac.uk/pdbsum/1e7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e7m ProSAT]</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=1e7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7m OCA], [https://pdbe.org/1e7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e7m RCSB], [https://www.ebi.ac.uk/pdbsum/1e7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e7m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G6PD_LEUME G6PD_LEUME]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1e7m ConSurf].
</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=1e7m ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The role of Asp-177 in the His-Asp catalytic dyad of glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides has been investigated by a structural and functional characterization of the D177N mutant enzyme. Its three-dimensional structure has been determined by X-ray cryocrystallography in the presence of NAD(+) and in the presence of glucose 6-phosphate plus NADPH. The structure of a glucose 6-phosphate complex of a mutant (Q365C) with normal enzyme activity has also been determined and substrate binding compared. To understand the effect of Asp-177 on the ionization properties of the catalytic base His-240, the pH dependence of kinetic parameters has been determined for the D177N mutant and compared to that of the wild-type enzyme. The structures give details of glucose 6-phosphate binding and show that replacement of the Asp-177 of the catalytic dyad with asparagine does not affect the overall structure of glucose 6-phosphate dehydrogenase. Additionally, the evidence suggests that the productive tautomer of His-240 in the D177N mutant enzyme is stabilized by a hydrogen bond with Asn-177; hence, the mutation does not affect tautomer stabilization. We conclude, therefore, that the absence of a negatively charged aspartate at 177 accounts for the decrease in catalytic activity at pH 7.8. Structural analysis suggests that the pH dependence of the kinetic parameters of D177N glucose 6-phosphate dehydrogenase results from an ionized water molecule replacing the missing negative charge of the mutated Asp-177 at high pH. Glucose 6-phosphate binding orders and orients His-178 in the D177N-glucose 6-phosphate-NADPH ternary complex and appears to be necessary to form this water-binding site.
An examination of the role of asp-177 in the His-Asp catalytic dyad of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase: X-ray structure and pH dependence of kinetic parameters of the D177N mutant enzyme.,Cosgrove MS, Gover S, Naylor CE, Vandeputte-Rutten L, Adams MJ, Levy HR Biochemistry. 2000 Dec 12;39(49):15002-11. PMID:11106478<ref>PMID:11106478</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1e7m" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Glucose 6-phosphate dehydrogenase|Glucose 6-phosphate dehydrogenase]]
*[[Glucose 6-phosphate dehydrogenase|Glucose 6-phosphate dehydrogenase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ascococcus mesenteroides tsenkovskii 1878]]
[[Category: Glucose-6-phosphate dehydrogenase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Adams, M J]]
[[Category: Leuconostoc mesenteroides]]
[[Category: Cosgrove, M S]]
[[Category: Adams MJ]]
[[Category: Gover, S]]
[[Category: Cosgrove MS]]
[[Category: Glucose metabolism]]
[[Category: Gover S]]
[[Category: Oxidoreductase]]

Latest revision as of 12:59, 20 March 2024

ACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDESACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES

Structural highlights

1e7m is a 1 chain structure with sequence from Leuconostoc mesenteroides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.54Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G6PD_LEUME

Evolutionary Conservation

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

See Also

1e7m, resolution 2.54Å

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