|
|
| (11 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1qbi.gif|left|200px]] | |
| | | | |
| - | {{Structure
| + | ==SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS== |
| - | |PDB= 1qbi |SIZE=350|CAPTION= <scene name='initialview01'>1qbi</scene>, resolution 1.72Å
| + | <StructureSection load='1qbi' size='340' side='right'caption='[[1qbi]], [[Resolution|resolution]] 1.72Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene> | + | <table><tr><td colspan='2'>[[1qbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_calcoaceticus Acinetobacter calcoaceticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBI FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Quinoprotein_glucose_dehydrogenase Quinoprotein glucose dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.5.2 1.1.5.2] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbi OCA], [https://pdbe.org/1qbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qbi RCSB], [https://www.ebi.ac.uk/pdbsum/1qbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbi ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbi OCA], [http://www.ebi.ac.uk/pdbsum/1qbi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qbi RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/DHGB_ACICA DHGB_ACICA] Oxidizes glucose to gluconolactone. |
| - | | + | == Evolutionary Conservation == |
| - | '''SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qbi_consurf.spt"</scriptWhenChecked> |
| - | The crystal structure of a dimeric apo form of the soluble quinoprotein glucose dehydrogenase (s-GDH) from Acinetobacter calcoaceticus has been solved by multiple isomorphous replacement followed by density modification, and was subsequently refined at 1. 72 A resolution to a final crystallographic R-factor of 16.5% and free R-factor of 20.8% [corrected]. The s-GDH monomer has a beta-propeller fold consisting of six four-stranded anti-parallel beta-sheets aligned around a pseudo 6-fold symmetry axis. The enzyme binds three calcium ions per monomer, two of which are located in the dimer interface. The third is bound in the putative active site, where it may bind and functionalize the pyrroloquinoline quinone (PQQ) cofactor. A data base search unexpectedly showed that four uncharacterized protein sequences are homologous to s-GDH with many residues in the putative active site absolutely conserved. This indicates that these homologs may have a similar structure and that they may catalyze similar PQQ-dependent reactions.A structure-based sequence alignment of the six four-stranded beta-sheets in s-GDH's beta-propeller fold shows an internally conserved sequence repeat that gives rise to two distinct conserved structural motifs. The first structural motif is found at the corner of the short beta-turn between the inner two beta-strands of the beta-sheets, where an Asp side-chain points back into the beta-sheet to form a hydrogen-bond with the OH/NH of a Tyr/Trp side-chain in the same beta-sheet. The second motif involves an Arg/Lys side-chain in the C beta-strand of one beta-sheet, which forms a bidentate salt-bridge with an Asp/Glu in the CD loop of the next beta-sheet. These intra and inter-beta-sheet hydrogen-bonds are likely to contribute to the stability of the s-GDH beta-propeller fold.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1QBI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_calcoaceticus Acinetobacter calcoaceticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBI OCA].
| + | </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=1qbi ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference==
| + | __TOC__ |
| - | The 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat., Oubrie A, Rozeboom HJ, Kalk KH, Duine JA, Dijkstra BW, J Mol Biol. 1999 Jun 4;289(2):319-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10366508 10366508]
| + | </StructureSection> |
| | [[Category: Acinetobacter calcoaceticus]] | | [[Category: Acinetobacter calcoaceticus]] |
| - | [[Category: Quinoprotein glucose dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Dijkstra BW]] |
| - | [[Category: Dijkstra, B W.]] | + | [[Category: Duine JA]] |
| - | [[Category: Duine, J A.]] | + | [[Category: Kalk KH]] |
| - | [[Category: Kalk, K H.]] | + | [[Category: Oubrie A]] |
| - | [[Category: Oubrie, A.]] | + | [[Category: Rozeboom HJ]] |
| - | [[Category: Rozeboom, H J.]] | + | |
| - | [[Category: beta-propeller]]
| + | |
| - | [[Category: superbarrel]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:11:25 2008''
| + | |
