2b5v: Difference between revisions

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New page: left|200px<br /><applet load="2b5v" size="350" color="white" frame="true" align="right" spinBox="true" caption="2b5v, resolution 2.00Å" /> '''Crystal structure of...
 
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[[Image:2b5v.gif|left|200px]]<br /><applet load="2b5v" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2b5v, resolution 2.00&Aring;" />
'''Crystal structure of glucose dehydrogenase from Haloferax mediterranei'''<br />


==Overview==
==Crystal structure of glucose dehydrogenase from Haloferax mediterranei==
The structure of glucose dehydrogenase from the extreme halophile, Haloferax mediterranei has been solved at 1.6-A resolution under, crystallization conditions which closely mimic the "in vivo" intracellular, environment. The decoration of the enzyme's surface with acidic residues, is only partially neutralized by bound potassium counterions, which also, appear to play a role in substrate binding. The surface shows the expected, reduction in hydrophobic character, surprisingly not from changes, associated with the loss of exposed hydrophobic residues but rather, arising from a loss of lysines consistent with the genome wide-reduction, of this residue in extreme halophiles. The structure reveals a highly, ordered, multilayered solvation shell that can be seen to be organized, into one dominant network covering much of the exposed surface accessible, area to an extent not seen in almost any other protein structure solved., This finding is consistent with the requirement of the enzyme to form a, protective shell in a dehydrating environment.
<StructureSection load='2b5v' size='340' side='right'caption='[[2b5v]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2b5v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5V FirstGlance]. <br>
2B5V is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei] with <scene name='pdbligand=NAP:'>NAP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5V OCA].
</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&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b5v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5v OCA], [https://pdbe.org/2b5v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5v RCSB], [https://www.ebi.ac.uk/pdbsum/2b5v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5v ProSAT]</span></td></tr>
Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei., Britton KL, Baker PJ, Fisher M, Ruzheinikov S, Gilmour DJ, Bonete MJ, Ferrer J, Pire C, Esclapez J, Rice DW, Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4846-51. Epub 2006 Mar 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16551747 16551747]
</table>
[[Category: Glucose 1-dehydrogenase]]
== Function ==
[https://www.uniprot.org/uniprot/GLCDH_HALMT GLCDH_HALMT] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>
== 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/b5/2b5v_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=2b5v ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Haloferax mediterranei]]
[[Category: Haloferax mediterranei]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Baker, P.J.]]
[[Category: Baker PJ]]
[[Category: Bonete, M.J.]]
[[Category: Bonete M-J]]
[[Category: Britton, K.L.]]
[[Category: Britton KL]]
[[Category: Esclapez, J.]]
[[Category: Esclapez J]]
[[Category: Ferrer, J.]]
[[Category: Ferrer J]]
[[Category: Fisher, M.]]
[[Category: Fisher M]]
[[Category: Gilmour, D.J.]]
[[Category: Gilmour DJ]]
[[Category: Pire, C.]]
[[Category: Pire C]]
[[Category: Rice, D.W.]]
[[Category: Rice DW]]
[[Category: Ruzheinikov, S.]]
[[Category: Ruzheinikov S]]
[[Category: NAP]]
[[Category: nucleotide binding motif]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:17:31 2008''

Latest revision as of 09:16, 14 February 2024

Crystal structure of glucose dehydrogenase from Haloferax mediterranei

2b5v, resolution 2.00Å

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