1
|
Prangé T, Girard E, Fourme R, Dhaussy A, Edwards B, Vaishnav A, Patel C, Guy‐Evans H, Hervé G, Evans DR. Pressure‐induced activation of latent dihydroorotase from Aquifex aeolicusas revealed by high pressure protein crystallography. FEBS J 2019; 286:1204-1213. [DOI: 10.1111/febs.14758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/19/2018] [Accepted: 01/15/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Thierry Prangé
- Laboratoire de Cristallographie & RMN biologiques (UMR 8015 CNRS) Paris France
| | - Eric Girard
- CEA CNRS IBS Université Grenoble Alpes France
| | - Roger Fourme
- Synchrotron SOLEIL L'Orme des Merisiers Saint‐Aubin France
| | | | - Brian Edwards
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| | - Asmita Vaishnav
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| | - Chandni Patel
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| | - Hedeel Guy‐Evans
- Department of Chemistry Eastern Michigan University Ypsilanti MI USA
| | - Guy Hervé
- Laboratoire BIOSIPE Sorbonne Université Institut de Biologie Paris Seine Université Pierre et Marie Curie Paris France
| | - David R. Evans
- Department of Biochemistry and Molecular Biology Wayne State University School of Medicine Detroit MI USA
| |
Collapse
|
2
|
Hervé G, Evans HG, Fernado R, Patel C, Hachem F, Evans DR. Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure. J Biol Chem 2017; 292:629-637. [PMID: 27746403 DOI: 10.1074/jbc.m116.739862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/14/2016] [Indexed: 01/12/2023] Open
Abstract
Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO), which catalyzes the third step in de novo pyrimidine biosynthesis. The isolated protein, a 45-kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates. The loop is mostly disordered but is tethered to the active site region by several electrostatic and hydrogen bonds. This loop becomes ordered and is displaced from the active site upon formation of DHO-ATC complex. The application of pressure to the complex causes its time-dependent dissociation and the loss of both DHO and ATC activities. Pressure induced irreversible dissociation of the obligate ATC trimer, and as a consequence the DHO is also inactivated. However, moderate hydrostatic pressure applied to the isolated DHO subunit mimics the complex formation and reversibly activates the isolated subunit in the absence of ATC, suggesting that the loop has been displaced from the active site. This effect of pressure is explained by the negative volume change associated with the disruption of ionic interactions and exposure of ionized amino acids to the solvent (electrostriction). The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues.
Collapse
Affiliation(s)
- Guy Hervé
- From the Laboratoire BIOSIPE, Sorbonne Universités, Institut de Biologie Paris Seine, CNRS, Université Pierre et Marie Curie, 75005 Paris, France,
| | - Hedeel Guy Evans
- the Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan 48197, and.,the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Roshini Fernado
- the Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan 48197, and
| | - Chandni Patel
- the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Fatme Hachem
- the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - David R Evans
- the Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan 48201
| |
Collapse
|
3
|
Aughey GN, Tastan ÖY, Liu JL. Cellular serpents and dreaming spires: new frontiers in arginine and pyrimidine biology. J Genet Genomics 2014; 41:561-5. [PMID: 25438702 DOI: 10.1016/j.jgg.2014.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/30/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Gabriel N Aughey
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ömür Y Tastan
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom.
| |
Collapse
|
4
|
Evans HG, Fernando R, Vaishnav A, Kotichukkala M, Heyl D, Hachem F, Brunzelle JS, Edwards BFP, Evans DR. Intersubunit communication in the dihydroorotase-aspartate transcarbamoylase complex of Aquifex aeolicus. Protein Sci 2014; 23:100-9. [PMID: 24353170 DOI: 10.1002/pro.2396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 11/01/2013] [Accepted: 11/01/2013] [Indexed: 11/06/2022]
Abstract
Aspartate transcarbamoylase and dihydroorotase, enzymes that catalyze the second and third step in de novo pyrimidine biosynthesis, are associated in dodecameric complexes in Aquifex aeolicus and many other organisms. The architecture of the dodecamer is ideally suited to channel the intermediate, carbamoyl aspartate from its site of synthesis on the ATC subunit to the active site of DHO, which catalyzes the next step in the pathway, because both reactions occur within a large, internal solvent-filled cavity. Channeling usually requires that the reactions of the enzymes are coordinated so that the rate of synthesis of the intermediate matches its rate of utilization. The linkage between the ATC and DHO subunits was demonstrated by showing that the binding of the bisubstrate analog, N-phosphonacetyl-L-aspartate to the ATC subunit inhibits the activity of the distal DHO subunit. Structural studies identified a DHO loop, loop A, interdigitating between the ATC domains that would be expected to interfere with domain closure essential for ATC catalysis. Mutation of the DHO residues in loop A that penetrate deeply between the two ATC domains inhibits the ATC activity by interfering with the normal reciprocal linkage between the two enzymes. Moreover, a synthetic peptide that mimics that part of the DHO loop that binds between the two ATC domains was found to be an allosteric or noncompletive ATC inhibitor (K(i) = 22 μM). A model is proposed suggesting that loop A is an important component of the functional linkage between the enzymes.
Collapse
Affiliation(s)
- Hedeel Guy Evans
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, 48197; Department of Biochemistry and Molecular Biology, Wayne State University, School of Medicine, Detroit, Michigan, 48201
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
The mononuclear metal center of type-I dihydroorotase from Aquifex aeolicus. BMC BIOCHEMISTRY 2013; 14:36. [PMID: 24314009 PMCID: PMC3880350 DOI: 10.1186/1471-2091-14-36] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 10/28/2013] [Indexed: 01/22/2023]
Abstract
BACKGROUND Dihydroorotase (DHO) is a zinc metalloenzyme, although the number of active site zinc ions has been controversial. E. coli DHO was initially thought to have a mononuclear metal center, but the subsequent X-ray structure clearly showed two zinc ions, α and β, at the catalytic site. Aquifex aeolicus DHO, is a dodecamer comprised of six DHO and six aspartate transcarbamoylase (ATC) subunits. The isolated DHO monomer, which lacks catalytic activity, has an intact α-site and conserved β-site ligands, but the geometry of the second metal binding site is completely disrupted. However, the putative β-site is restored when the complex with ATC is formed and DHO activity is regained. Nevertheless, the X-ray structure of the complex revealed a single zinc ion at the active site. The structure of DHO from the pathogenic organism, S. aureus showed that it also has a single active site metal ion. RESULTS Zinc analysis showed that the enzyme has one zinc/DHO subunit and the addition of excess metal ion did not stimulate catalytic activity, nor alter the kinetic parameters. The metal free apoenzyme was inactive, but the full activity was restored upon the addition of one equivalent of Zn2+ or Co2+. Moreover, deletion of the β-site by replacing the His180 and His232 with alanine had no effect on catalysis in the presence or absence of excess zinc. The 2.2 Å structure of the double mutant confirmed that the β-site was eliminated but that the active site remained otherwise intact. CONCLUSIONS Thus, kinetically competent A. aeolicus DHO has a mononuclear metal center. In contrast, elimination of the putative second metal binding site in amidohydrolyases with a binuclear metal center, resulted in the abolition of catalytic activity. The number of active site metal ions may be a consideration in the design of inhibitors that selectively target either the mononuclear or binuclear enzymes.
Collapse
|
6
|
Purcarea C, Fernando R, Evans HG, Evans DR. The sole serine/threonine protein kinase and its cognate phosphatase from Aquifex aeolicus targets pyrimidine biosynthesis. Mol Cell Biochem 2008; 311:199-213. [PMID: 18270660 DOI: 10.1007/s11010-008-9710-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2007] [Accepted: 01/10/2008] [Indexed: 10/22/2022]
Abstract
Serine/Threonine kinases participate in complex, interacting signaling pathways in eukaryotes, prokaryotes, and archae. While most organisms contain many different kinases, the extreme hyperthermophile, Aquifex aeolicus encodes a single hypothetical Ser/Thr kinase. A gene homologous to eukaryotic protein phosphatases overlaps the kinase gene by a single base pair. The putative kinase, AaSTPK and phosphatase, AaPPM, were cloned and expressed in E. coli, purified to homogeneity and found to be functional. AaSTPK is a 34-kDa monomer that can use MgATP, MnATP, or MnGTP as co-substrates, although MgATP appears to be the preferred substrate. AaSTPK was autophosphorylated on a threonine residue and was dephosphorylated by AaPPM. AaPPM phosphatase is homologous to the PPM sub-family of Ser/Thr phosphatases and was stimulated by MnCl2 and CoCl2 but not MgCl2. AaSTPK also phosphorylated one threonine residue on the carbamoyl phosphate synthetase, CPS.A subunit. Carbamoyl phosphate synthetase reconstituted with phosphorylated CPS.A had unaltered catalytic activity but allosteric inhibition by UMP and activation by the arginine intermediate, ornithine, were both appreciably attenuated. These changes in allosteric regulation would be expected to activate pyrimidine biosynthesis by releasing the constraints imposed on carbamoyl phosphate synthetase activity by UMP and uncoupling the regulation of pyrimidine and arginine biosynthesis. CPS.A was also dephosphorylated by AaPPM. Aquifex aeolicus occupies the lowest branch on the prokaryotic phylogenetic tree. The Thr/Ser kinase, its cognate phosphatase and a protein substrate may be elements of a simple signaling pathway, perhaps the most primitive example of this mode of regulation described thus far.
Collapse
Affiliation(s)
- Cristina Purcarea
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 E. Canfield Street, Detroit, MI 48201, USA
| | | | | | | |
Collapse
|
7
|
Martin PD, Purcarea C, Zhang P, Vaishnav A, Sadecki S, Guy-Evans HI, Evans DR, Edwards BFP. The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex aeolicus at 1.7Å Resolution. J Mol Biol 2005; 348:535-47. [PMID: 15826652 DOI: 10.1016/j.jmb.2005.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 02/28/2005] [Accepted: 03/03/2005] [Indexed: 11/16/2022]
Abstract
Dihydroorotases (EC 3.5.2.3) catalyze the reversible cyclization of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. The X-ray structures of Aquifex aeolicus dihydroorotase in two space groups, C222(1) and C2, were determined at a resolution of 1.7A. These are the first structures of a type I dihydroorotase, a class of molecules that includes the dihydroorotase domain of mammalian CAD. The type I enzymes are more ancient and larger, at 45 kDa, than the type II enzymes exemplified by the 38 kDa Escherichia coli dihydroorotase. Both dihydroorotases are members of the metallo-dependent hydrolase superfamily, whose members have a distorted "TIM barrel" domain containing the active site. However, A.aeolicus dihydroorotase has a second, composite domain, which the E.coli enzyme lacks and has only one of the two zinc atoms present in the E.coli enzyme. A.aeolicus dihydroorotase is unique in exhibiting significant activity only when complexed with aspartate transcarbamoylase, whereas the E.coli dihydroorotase and the CAD dihydroorotase domain are active as free proteins. The latency of A.aeolicus dihydroorotase can be related to two differences between its structure and that of E.coli dihydroorotase: (1) the monoclinic structure has a novel cysteine ligand to the zinc that blocks the active site and possibly functions as a "cysteine switch"; and (2) active site residues that bind the substrate in E.coli dihydroorotase are located in disordered loops in both crystal structures of A.aeolicus dihydroorotase and may function as a disorder-to-order "entropy switch".
Collapse
Affiliation(s)
- Philip D Martin
- Wayne State University School of Medicine, Department of Biochemistry and Molecular Biology, 540 E. Canfield, Detroit, MI 48201, USA
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Lee M, Chan CW, Mitchell Guss J, Christopherson RI, Maher MJ. Dihydroorotase from Escherichia coli: Loop Movement and Cooperativity between Subunits. J Mol Biol 2005; 348:523-33. [PMID: 15826651 DOI: 10.1016/j.jmb.2005.01.067] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 01/20/2005] [Accepted: 01/26/2005] [Indexed: 11/29/2022]
Abstract
Escherichia coli dihydroorotase has been crystallized in the presence of the product, L-dihydroorotate (L-DHO), and the structure refined at 1.9A resolution. The structure confirms that previously reported (PDB entry 1J79), crystallized in the presence of the substrate N-carbamyl-D,L-aspartate (D, L-CA-asp), which had a dimer in the asymmetric unit, with one subunit having the substrate, L-CA-asp bound at the active site and the other having L-DHO. Importantly, no explanation for the unusual structure was given. Our results now show that a loop comprised of residues 105-115 has different conformations in the two subunits. In the case of the L-CA-asp-bound subunit, this loop reaches in toward the active site and makes hydrogen-bonding contact with the bound substrate molecule. For the L-DHO-bound subunit, the loop faces in the opposite direction and forms part of the surface of the protein. Analysis of the kinetics for conversion of L-DHO to L-CA-asp at low concentrations of L-DHO shows positive cooperativity with a Hill coefficient n=1.57(+/-0.13). Communication between subunits in the dimer may occur via cooperative conformational changes of the side-chains of a tripeptide from each subunit: Arg256-His257-Arg258, near the subunit interface.
Collapse
Affiliation(s)
- Mihwa Lee
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | | | | | | |
Collapse
|
9
|
Ahuja A, Purcarea C, Ebert R, Sadecki S, Guy HI, Evans DR. Aquifex aeolicus dihydroorotase: association with aspartate transcarbamoylase switches on catalytic activity. J Biol Chem 2004; 279:53136-44. [PMID: 15381710 DOI: 10.1074/jbc.m403009200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroorotase (DHOase) catalyzes the reversible condensation of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. The enzyme from Aquifex aeolicus, a hyperthermophilic organism of ancient lineage, was cloned and expressed in Escherichia coli. The purified protein was found to be a 45-kDa monomer containing a single zinc ion. Although there is no other DHOase gene in the A. aeolicus genome, the recombinant protein completely lacked catalytic activity at any temperature tested. However, DHOase formed an active complex with aspartate transcarbamoylase (ATCase) from the same organism. Whereas the k(cat) of 13.8 +/- 0.03 s(-1) was close to the value observed for the mammalian enzyme, the K (m)for dihydroorotate, 3.03 +/- 0.05 mM was 433-fold higher. Gel filtration and chemical cross-linking showed that the complex exists as a 240-kDa hexamer (DHO(3)-ATC(3)) and a 480-kDa duodecamer (DHO(6)-ATC(6)) probably in rapid equilibrium. Complex formation protects both DHOase and ATCase against thermal degradation at temperatures near 100 degrees C where the organism grows optimally. These results lead to the reclassification of both enzymes: ATCase, previously considered a Class C homotrimer, now falls into Class A, whereas the DHOase is a Class 1B enzyme. CD spectroscopy indicated that association with ATCase does not involve a significant perturbation of the DHOase secondary structure, but the visible absorption spectrum of a Co(2+)-substituted DHOase is appreciably altered upon complex formation suggesting a change in the electronic environment of the active site. The association of DHOase with ATCase probably serves as a molecular switch that ensures that free, uncomplexed DHOase in the cell remains inactive. At pH 7.4, the equilibrium ratio of carbamoyl aspartate to dihydroorotate is 17 and complex formation may drive the reaction in the biosynthetic direction.
Collapse
Affiliation(s)
- Anupama Ahuja
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 E. Canfield St., Detroit, MI 48201, USA
| | | | | | | | | | | |
Collapse
|