This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1qbi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:14, 14 February 2024) (edit) (undo)
 
(12 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 1.72&Aring;
+
<StructureSection load='1qbi' size='340' side='right'caption='[[1qbi]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</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= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.72&#8491;</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>
-
}}
+
<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>
-
 
+
</table>
-
'''SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/DHGB_ACICA DHGB_ACICA] Oxidizes glucose to gluconolactone.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
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.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qbi_consurf.spt"</scriptWhenChecked>
-
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].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
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]
+
</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>
 +
__TOC__
 +
</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: CA]]
+
-
[[Category: GOL]]
+
-
[[Category: PT]]
+
-
[[Category: beta-propeller]]
+
-
[[Category: superbarrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:35:30 2008''
+

Current revision

SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS

PDB ID 1qbi

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qbi"
Personal tools