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Štěpánková A, Dušková J, Skálová T, Hašek J, Koval’ T, Østergaard LH, Dohnálek J. Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:346-54. [PMID: 23545636 PMCID: PMC3614155 DOI: 10.1107/s1744309113002674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/27/2013] [Indexed: 11/10/2022]
Abstract
The bacterial enzyme organophosphorus acid anhydrolase (OPAA) is able to catalyze the hydrolysis of both proline dipeptides (Xaa-Pro) and several types of organophosphate (OP) compounds. The full three-dimensional structure of the manganese-dependent OPAA enzyme is presented for the first time. This enzyme, which was originally isolated from the marine bacterium Alteromonas macleodii, was prepared recombinantly in Escherichia coli. The crystal structure was determined at 1.8 Å resolution in space group C2, with unit-cell parameters a = 133.8, b = 49.2, c = 97.3 Å, β = 125.0°. The enzyme forms dimers and their existence in solution was confirmed by dynamic light scattering and size-exclusion chromatography. The enzyme shares the pita-bread fold of its C-terminal domain with related prolidases. The binuclear manganese centre is located in the active site within the pita-bread domain. Moreover, an Ni(2+) ion from purification was localized according to anomalous signal. This study presents the full structure of this enzyme with complete surroundings of the active site and provides a critical analysis of its relationship to prolidases.
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Affiliation(s)
- Andrea Štěpánková
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, CTU in Prague, Trojanova 13, 120 00 Prague 2, Czech Republic
| | - Jarmila Dušková
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | - Tereza Skálová
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | - Jindřich Hašek
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | - Tomáš Koval’
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
| | | | - Jan Dohnálek
- Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovsky sq. 2, 162 06 Prague 6, Czech Republic
- Institute of Physics, AS CR, v.v.i., Na Slovance 2, 182 21 Prague 8, Czech Republic
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Kolenko P, Rozbeský D, Vaněk O, Bezouška K, Hašek J, Dohnálek J. Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1519-23. [PMID: 22139156 PMCID: PMC3232129 DOI: 10.1107/s1744309111046203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 11/02/2011] [Indexed: 11/11/2022]
Abstract
The structure of the H107R variant of the extracellular domain of the mouse natural killer cell receptor NKR-P1A has been determined by X-ray diffraction at 2.3 Å resolution from a merohedrally twinned crystal. Unlike the structure of the wild-type receptor in space group I4(1)22 with a single chain per asymmetric unit, the crystals of the variant belonged to space group I4(1) with a dimer in the asymmetric unit. Different degrees of merohedral twinning were detected in five data sets collected from different crystals. The mutation does not have a significant impact on the overall structure, but led to the binding of an additional phosphate ion at the interface of the molecules.
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Affiliation(s)
- Petr Kolenko
- Institute of Macromolecular Chemistry AS CR, vvi, Prague, Czech Republic.
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Kolenko P, Rozbeský D, Vaněk O, Kopecký V, Hofbauerová K, Novák P, Pompach P, Hašek J, Skálová T, Bezouška K, Dohnálek J. Molecular architecture of mouse activating NKR-P1 receptors. J Struct Biol 2011; 175:434-41. [PMID: 21600988 DOI: 10.1016/j.jsb.2011.05.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/28/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
Receptors belonging to NKR-P1 family and their specific Clr ligands form an alternative missing self recognition system critical in immunity against tumors and viruses, elimination of tumor cells subjected to genotoxic stress, activation of T cell dependent immune response, and hypertension. The three-dimensional structure of the extracellular domain of the mouse natural killer (NK) cell receptor mNKR-P1Aex has been determined by X-ray diffraction. The core of the C-type lectin domain (CTLD) is homologous to the other CTLD receptors whereas one quarter of the domain forms an extended loop interacting tightly with a neighboring loop in the crystal. This domain swapping mechanism results in a compact interaction interface. A second dimerization interface resembles the known arrangement of other CTLD NK receptors. A functional dimeric form of the receptor is suggested, with the loop, evolutionarily conserved within this family, proposed to participate in interactions with ligands.
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Affiliation(s)
- Petr Kolenko
- Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 16206 Prague 6, Czech Republic
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