1qbi
From Proteopedia
(New page: 200px<br /><applet load="1qbi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qbi, resolution 1.72Å" /> '''SOLUBLE QUINOPROTEIN...) |
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| - | [[Image:1qbi.gif|left|200px]]<br /><applet load="1qbi" size=" | + | [[Image:1qbi.gif|left|200px]]<br /><applet load="1qbi" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1qbi, resolution 1.72Å" /> | caption="1qbi, resolution 1.72Å" /> | ||
'''SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS'''<br /> | '''SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of a dimeric apo form of the soluble quinoprotein | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1QBI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_calcoaceticus Acinetobacter calcoaceticus] with PT, CA and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http:// | + | 1QBI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acinetobacter_calcoaceticus Acinetobacter calcoaceticus] with <scene name='pdbligand=PT:'>PT</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QBI OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Quinoprotein glucose dehydrogenase]] | [[Category: Quinoprotein glucose dehydrogenase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Dijkstra, B | + | [[Category: Dijkstra, B W.]] |
| - | [[Category: Duine, J | + | [[Category: Duine, J A.]] |
| - | [[Category: Kalk, K | + | [[Category: Kalk, K H.]] |
[[Category: Oubrie, A.]] | [[Category: Oubrie, A.]] | ||
| - | [[Category: Rozeboom, H | + | [[Category: Rozeboom, H J.]] |
[[Category: CA]] | [[Category: CA]] | ||
[[Category: GOL]] | [[Category: GOL]] | ||
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[[Category: superbarrel]] | [[Category: superbarrel]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:37:56 2008'' |
Revision as of 12:37, 21 February 2008
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SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS
Overview
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.
About this Structure
1QBI is a Single protein structure of sequence from Acinetobacter calcoaceticus with , and as ligands. Active as Quinoprotein glucose dehydrogenase, with EC number 1.1.5.2 Full crystallographic information is available from OCA.
Reference
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:10366508
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