2b5w

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei

Structural highlights

2b5w is a 1 chain structure with sequence from Haloferax mediterranei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2]

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 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.

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:16551747^[3]

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

References

↑ Pire C, Esclapez J, Ferrer J, Bonete MJ. Heterologous overexpression of glucose dehydrogenase from the halophilic archaeon Haloferax mediterranei, an enzyme of the medium chain dehydrogenase/reductase family. FEMS Microbiol Lett. 2001 Jun 25;200(2):221-7. PMID:11425479
↑ Bonete MJ, Pire C, LLorca FI, Camacho ML. Glucose dehydrogenase from the halophilic Archaeon Haloferax mediterranei: enzyme purification, characterisation and N-terminal sequence. FEBS Lett. 1996 Apr 1;383(3):227-9. PMID:8925901
↑ Britton KL, Baker PJ, Fisher M, Ruzheinikov S, Gilmour DJ, Bonete MJ, Ferrer J, Pire C, Esclapez J, Rice DW. Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4846-51. Epub 2006 Mar 21. PMID:16551747

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2b5w"

@@ Line 3: / Line 3: @@
 <StructureSection load='2b5w' size='340' side='right'caption='[[2b5w]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33500 Atcc 33500]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2b5w]] 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=2B5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6&#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;'>[[2b5v|2b5v]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gdh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [https://pdbe.org/2b5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [https://www.ebi.ac.uk/pdbsum/2b5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5w ProSAT]</span></td></tr>
 </table>
 == 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>
+[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]]
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 33500]]
+[[Category: Haloferax mediterranei]]
-[[Category: Glucose 1-dehydrogenase]]
 [[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: Nucleotide binding motif]]
-[[Category: Oxidoreductase]]

2b5w

From Proteopedia

Current revision

Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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