2vwp

From Proteopedia

(Difference between revisions)

Current revision

Haloferax mediterranei glucose dehydrogenase in complex with NADPH and Zn.

Structural highlights

2vwp 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 2.01Å
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

Despite being the subject of intensive investigations, many aspects of the mechanism of the zinc-dependent medium chain alcohol dehydrogenase (MDR) superfamily remain contentious. We have determined the high-resolution structures of a series of binary and ternary complexes of glucose dehydrogenase, an MDR enzyme from Haloferax mediterranei. In stark contrast to the textbook MDR mechanism in which the zinc ion is proposed to remain stationary and attached to a common set of protein ligands, analysis of these structures reveals that in each complex, there are dramatic differences in the nature of the zinc ligation. These changes arise as a direct consequence of linked movements of the zinc ion, a zinc-bound bound water molecule, and the substrate during progression through the reaction. These results provide evidence for the molecular basis of proton traffic during catalysis, a structural explanation for pentacoordinate zinc ion intermediates, a unifying view for the observed patterns of metal ligation in the MDR family, and highlight the importance of dynamic fluctuations at the metal center in changing the electrostatic potential in the active site, thereby influencing the proton traffic and hydride transfer events.

Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily.,Baker PJ, Britton KL, Fisher M, Esclapez J, Pire C, Bonete MJ, Ferrer J, Rice DW Proc Natl Acad Sci U S A. 2009 Jan 8. PMID:19131516^[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
↑ Baker PJ, Britton KL, Fisher M, Esclapez J, Pire C, Bonete MJ, Ferrer J, Rice DW. Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily. Proc Natl Acad Sci U S A. 2009 Jan 8. PMID:19131516 doi:0807529106

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/2vwp"

@@ Line 1: / Line 1: @@
-==HALOFERAX MEDITERRANEI GLUCOSE DEHYDROGENASE IN COMPLEX WITH NADPH AND ZN.==
-<StructureSection load='2vwp' size='340' side='right' caption='[[2vwp]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+==Haloferax mediterranei glucose dehydrogenase in complex with NADPH and Zn.==
+<StructureSection load='2vwp' size='340' side='right'caption='[[2vwp]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vwp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VWP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vwp]] 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=2VWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VWP FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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]] 2.01&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vwg|2vwg]], [[2b5w|2b5w]], [[2b5v|2b5v]], [[2vwh|2vwh]], [[2vwq|2vwq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=2vwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwp OCA], [https://pdbe.org/2vwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vwp RCSB], [https://www.ebi.ac.uk/pdbsum/2vwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vwp ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vwp RCSB], [http://www.ebi.ac.uk/pdbsum/2vwp PDBsum]</span></td></tr>
+</table>
-<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>
 == 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/vw/2vwp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vw/2vwp_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/chain_selection.php?pdb_ID=2ata 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=2vwp ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vwp" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Glucose 1-dehydrogenase]]
 [[Category: Haloferax mediterranei]]
-[[Category: Baker, P J.]]
+[[Category: Large Structures]]
-[[Category: Bonete, M J.]]
+[[Category: Baker PJ]]
-[[Category: Britton, K L.]]
+[[Category: Bonete MJ]]
-[[Category: Esclapez, J.]]
+[[Category: Britton KL]]
-[[Category: Ferrer, J.]]
+[[Category: Esclapez J]]
-[[Category: Fisher, M.]]
+[[Category: Ferrer J]]
-[[Category: Pire, C.]]
+[[Category: Fisher M]]
-[[Category: Rice, D W.]]
+[[Category: Pire C]]
-[[Category: Alcohol dehydrogenase]]
+[[Category: Rice DW]]
-[[Category: Glucose dehydrogenase]]
-[[Category: Oxidoreductase]]
-[[Category: Zinc dependent medium chain alcohol dehydrogenase family]]

2vwp

From Proteopedia

Current revision

Haloferax mediterranei glucose dehydrogenase in complex with NADPH and Zn.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox