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Wosicki S, Kazmierczyk M, Gilski M, Zabranska H, Pichova I, Jaskolski M. Crystal structures of inhibitor complexes of M-PMV protease with visible flap loops. Protein Sci 2021; 30:1258-1263. [PMID: 33786913 PMCID: PMC8138519 DOI: 10.1002/pro.4072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/05/2022]
Abstract
Mason‐Pfizer monkey virus protease (PR) was crystallized in complex with two pepstatin‐based inhibitors in P1 space group. In both crystal structures, the extended flap loops that lock the inhibitor/substrate over the active site, are visible in the electron density either completely or with only small gaps, providing the first observation of the conformation of the flap loops in dimeric complex form of this retropepsin. The H‐bond network in the active site (with D26N mutation) differs from that reported for the P21 crystal structures and is similar to a rarely occurring system in HIV‐1 PR. PDB Code(s): 7bgt and 7bgu;
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Affiliation(s)
- Stanislaw Wosicki
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Maciej Kazmierczyk
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Helena Zabranska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Iva Pichova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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Wosicki S, Gilski M, Zabranska H, Pichova I, Jaskolski M. Comparison of a retroviral protease in monomeric and dimeric states. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:904-917. [PMID: 31588922 DOI: 10.1107/s2059798319011355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022]
Abstract
Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason-Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S-S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.
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Affiliation(s)
- Stanislaw Wosicki
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Miroslaw Gilski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Helena Zabranska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Iva Pichova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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3
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Rumlová M, Křížová I, Hadravová R, Doležal M, Strohalmová K, Keprová A, Pichová I, Ruml T. Breast cancer-associated protein--a novel binding partner of Mason-Pfizer monkey virus protease. J Gen Virol 2014; 95:1383-1389. [PMID: 24659101 DOI: 10.1099/vir.0.064345-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We identified breast cancer-associated protein (BCA3) as a novel binding partner of Mason-Pfizer monkey virus (MPMV) protease (PR). The interaction was confirmed by co-immunoprecipitation and immunocolocalization of MPMV PR and BCA3. Full-length but not C-terminally truncated BCA3 was incorporated into MPMV virions. We ruled out the potential role of the G-patch domain, a glycine-rich domain located at the C terminus of MPMV PR, in BCA3 interaction and virion incorporation. Expression of BCA3 did not affect MPMV particle release and proteolytic processing; however, it slightly increased MPMV infectivity.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, Institute of Chemical Technology, Technická 5, 166 28 Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Ivana Křížová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Romana Hadravová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Michal Doležal
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Technická 5, 166 28 Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Karolína Strohalmová
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Technická 5, 166 28 Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Alena Keprová
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Technická 5, 166 28 Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., IOCB & Gilead Research Center, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Technická 5, 166 28 Prague, Czech Republic
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Gillet FX, Cattoni DI, Petiot-Bécard S, Delalande F, Poignavent V, Brizard JP, Bessin Y, Dorsselaer AV, Declerck N, Sanglier-Cianférani S, Brugidou C, Vignols F. The RYMV-Encoded Viral Suppressor of RNA Silencing P1 Is a Zinc-Binding Protein with Redox-Dependent Flexibility. J Mol Biol 2013; 425:2423-35. [DOI: 10.1016/j.jmb.2013.03.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/14/2013] [Accepted: 03/18/2013] [Indexed: 10/27/2022]
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The G-patch domain of Mason-Pfizer monkey virus is a part of reverse transcriptase. J Virol 2011; 86:1988-98. [PMID: 22171253 DOI: 10.1128/jvi.06638-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mason-Pfizer monkey virus (M-PMV), like some other betaretroviruses, encodes a G-patch domain (GPD). This glycine-rich domain, which has been predicted to be an RNA binding module, is invariably localized at the 3' end of the pro gene upstream of the pro-pol ribosomal frameshift sequence of genomic RNAs of betaretroviruses. Following two ribosomal frameshift events and the translation of viral mRNA, the GPD is present in both Gag-Pro and Gag-Pro-Pol polyproteins. During the maturation of the Gag-Pro polyprotein, the GPD transiently remains a C-terminal part of the protease (PR), from which it is then detached by PR itself. The destiny of the Gag-Pro-Pol-encoded GPD remains to be determined. The function of the GPD in the retroviral life cycle is unknown. To elucidate the role of the GPD in the M-PMV replication cycle, alanine-scanning mutational analysis of its most highly conserved residues was performed. A series of individual mutations as well as the deletion of the entire GPD had no effect on M-PMV assembly, polyprotein processing, and RNA incorporation. However, a reduction of the reverse transcriptase (RT) activity, resulting in a drop in M-PMV infectivity, was determined for all GPD mutants. Immunoprecipitation experiments suggested that the GPD is a part of RT and participates in its function. These data indicate that the M-PMV GPD functions as a part of reverse transcriptase rather than protease.
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Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M. High-resolution structure of a retroviral protease folded as a monomer. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:907-14. [PMID: 22101816 PMCID: PMC3211970 DOI: 10.1107/s0907444911035943] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/03/2011] [Indexed: 11/10/2022]
Abstract
Mason-Pfizer monkey virus (M-PMV), a D-type retrovirus assembling in the cytoplasm, causes simian acquired immunodeficiency syndrome (SAIDS) in rhesus monkeys. Its pepsin-like aspartic protease (retropepsin) is an integral part of the expressed retroviral polyproteins. As in all retroviral life cycles, release and dimerization of the protease (PR) is strictly required for polyprotein processing and virion maturation. Biophysical and NMR studies have indicated that in the absence of substrates or inhibitors M-PMV PR should fold into a stable monomer, but the crystal structure of this protein could not be solved by molecular replacement despite countless attempts. Ultimately, a solution was obtained in mr-rosetta using a model constructed by players of the online protein-folding game Foldit. The structure indeed shows a monomeric protein, with the N- and C-termini completely disordered. On the other hand, the flap loop, which normally gates access to the active site of homodimeric retropepsins, is clearly traceable in the electron density. The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins. The overall fold of the protein follows the retropepsin canon, but the C(α) deviations are large and the active-site 'DTG' loop (here NTG) deviates up to 2.7 Å from the standard conformation. This structure of a monomeric retropepsin determined at high resolution (1.6 Å) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including AIDS.
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Affiliation(s)
- Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Maciej Kazmierczyk
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland
| | - Szymon Krzywda
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland
| | - Helena Zábranská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Seth Cooper
- Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
| | - Zoran Popović
- Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA
| | - Firas Khatib
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
| | - James Thompson
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA 98195, USA
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Premature processing of mouse mammary tumor virus Gag polyprotein impairs intracellular capsid assembly. Virology 2008; 384:33-7. [PMID: 19046754 DOI: 10.1016/j.virol.2008.10.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 04/09/2008] [Accepted: 10/24/2008] [Indexed: 11/24/2022]
Abstract
Mouse mammary tumor virus (MMTV) is the prototypical member of the Betaretrovirus genus, but the processes of its morphogenesis are poorly characterized. In this report, we describe an unusual intracellular processing of MMTV Gag polyprotein in human 293T cells transiently expressing MMTV from heterologous promoter. The same specific cleavage products of the viral protease were seen for the wild type as well as for nonmyristylated mutant of MMTV Gag polyprotein completely defective in the particle release. Inactivation of the viral protease resulted in more stable Gag polyprotein and in accumulation of intracytoplasmic particles for nonmyristylated Gag. The intracellular processing of nonmyristylated MMTV Gag indicates that protease activation in betaretrovirus can occur independently of budding.
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Hartl MJ, Wöhrl BM, Rösch P, Schweimer K. The solution structure of the simian foamy virus protease reveals a monomeric protein. J Mol Biol 2008; 381:141-9. [PMID: 18597783 DOI: 10.1016/j.jmb.2008.05.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 10/22/2022]
Abstract
In contrast to orthoretroviruses, foamy viruses (FVs) express their Pol polyprotein from a separate pol-specific transcript. Only the integrase domain is cleaved off, leading to a protease-reverse transcriptase (PR-RT) protein. We purified the separate PR domain (PRshort) of simian FV from macaques by expressing the recombinant gene in Escherichia coli. Sedimentation analyses and size exclusion chromatography indicate that PRshort is a stable monomer in solution. This allowed us to determine the structure of the PRshort monomer using 1426 experimental restraints derived from NMR spectroscopy. The superposition of 20 conformers resulted in a backbone atom rmsd of 0.55 A for residues Gln8-Leu93. Although the overall folds are similar, the macaque simian FV PRshort reveals significant differences in the dimerization interface relative to other retroviral PRs, such as HIV-1 (human immunodeficiency virus type 1) PR, which appear to be rather stable dimers. Especially the flap region and the N- and C-termini of PRshort are highly flexible. Neglecting these regions, the backbone atom rmsd drops to 0.32 A, highlighting the good definition of the central part of the protein. To exclude that the monomeric state of PRshort is due to cleaving off the RT, we purified the complete PR-RT and performed size exclusion chromatography. Our data show that PR-RT is also monomeric. We thus conclude adoption of a monomeric state of PR-RT to be a regulatory mechanism to inhibit PR activity before virus assembly in order to reduce packaging problems. Dimerization might therefore be triggered by additional viral or cellular factors.
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Affiliation(s)
- Maximilian J Hartl
- Lehrstuhl für Struktur und Chemie der Biopolymere, Universität Bayreuth, 95440 Bayreuth, Germany
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