5B6P

Structure of the dodecameric type-II dehydrogenate dehydratase from Acinetobacter baumannii at 2.00 A resolution

Replaces:  5IBA

Summary for 5B6P

• Entry DOI: 10.2210/pdb5b6p/pdb
• Descriptor: 3-dehydroquinate dehydratase, SULFATE ION (3 entities in total)
• Functional Keywords: lyase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 12
• Total formula weight: 199354.39

Authors

Kumar, M.,Iqbal, N.,Kaur, P.,Sharma, S.,Singh, T.P. (deposition date: 2016-05-31, release date: 2016-09-07, Last modification date: 2023-11-08)

Primary citation

Iqbal, N.,Kumar, M.,Sharma, P.,Yadav, S.P.,Kaur, P.,Sharma, S.,Singh, T.P.
Binding studies and structure determination of the recombinantly produced type-II 3-dehydroquinate dehydratase from Acinetobacter baumannii.
Int. J. Biol. Macromol., 94:459-465, 2017

PubMed Abstract: 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 2.0Å resolution. Crystals belonged to monoclinic space group P2 with cell dimensions, a=82.3, b=95.3, c=132.3Å and β=95.7°. The structure was solved with molecular replacement method and refined to values of 0.200 and 0.232 for R and R factors. The structures of 12 crystallographically independent molecules in the asymmetry unit were identical with r.m.s shifts for the C atoms ranging from 0.3Å to 0.8Å. 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.

PubMed: 27769928
DOI: 10.1016/j.ijbiomac.2016.10.049

Experimental method

X-RAY DIFFRACTION (2 Å)