5b6p
From Proteopedia
(Difference between revisions)
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==Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A resolution== | ==Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A resolution== | ||
| - | <StructureSection load='5b6p' size='340' side='right' caption='[[5b6p]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='5b6p' size='340' side='right'caption='[[5b6p]], [[Resolution|resolution]] 2.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5b6p]] is a 12 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5iba 5iba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B6P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5b6p]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Acibt Acibt]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5iba 5iba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B6P FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aroQ, A1S_2009 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=400667 ACIBT])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-dehydroquinate_dehydratase 3-dehydroquinate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.10 4.2.1.10] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-dehydroquinate_dehydratase 3-dehydroquinate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.10 4.2.1.10] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b6p OCA], [http://pdbe.org/5b6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b6p RCSB], [http://www.ebi.ac.uk/pdbsum/5b6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b6p ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b6p OCA], [http://pdbe.org/5b6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b6p RCSB], [http://www.ebi.ac.uk/pdbsum/5b6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b6p ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/AROQ_ACIBT AROQ_ACIBT]] Catalyzes a trans-dehydration via an enolate intermediate. | [[http://www.uniprot.org/uniprot/AROQ_ACIBT AROQ_ACIBT]] Catalyzes a trans-dehydration via an enolate intermediate. | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Dehydroquinase (3-dehydroquinate dehydratase, DHQD, EC 4.2.1.10) catalyzes the conversion of dehydroquinate to dehydroshikimate. DHQD from Acinetobacter baumannii (AbDHQD) was cloned, expressed and purified to homogeneity. The binding studies showed that two compounds quinic acid and citrazinic acid bound to AbDHQD at micromolar concentrations. AbDHQD was crystallized using 30% PEG-3350, 50mM tris-HCl and 1.0M MgSO4 at pH 8.0. Crystals of AbDHQD were stabilized with 25% glycerol for data collection at 100K. The X-ray intensity data were collected to 2.0A resolution. Crystals belonged to monoclinic space group P21 with cell dimensions, a=82.3, b=95.3, c=132.3A and beta=95.7 degrees . The structure was solved with molecular replacement method and refined to values of 0.200 and 0.232 for Rcryst and Rfree factors. The structures of 12 crystallographically independent molecules in the asymmetry unit were identical with r.m.s shifts for the C(alpha) atoms ranging from 0.3A to 0.8A. They formed a dodecamer with four trimers arranged in a tetrahedral manner. The classical lid adopted an open conformation although a sulfate ion was observed in the substrate binding site. As a result of which, the compounds quinic acid and citrazinic acid could not bind to AbDHQD. | ||
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| + | Binding studies and structure determination of the recombinantly produced type-II 3-dehydroquinate dehydratase from Acinetobacter baumannii.,Iqbal N, Kumar M, Sharma P, Yadav SP, Kaur P, Sharma S, Singh TP Int J Biol Macromol. 2017 Jan;94(Pt A):459-465. doi:, 10.1016/j.ijbiomac.2016.10.049. Epub 2016 Oct 18. PMID:27769928<ref>PMID:27769928</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5b6p" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Dehydroquinase|Dehydroquinase]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: 3-dehydroquinate dehydratase]] | [[Category: 3-dehydroquinate dehydratase]] | ||
| + | [[Category: Acibt]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Iqbal, N]] | [[Category: Iqbal, N]] | ||
[[Category: Kaur, P]] | [[Category: Kaur, P]] | ||
Revision as of 06:19, 17 April 2019
Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A resolution
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