1
|
D'Andréa ÉD, Retel JS, Diehl A, Schmieder P, Oschkinat H, Pires JR. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. J Struct Biol 2021; 213:107715. [PMID: 33705979 DOI: 10.1016/j.jsb.2021.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
The 106-residue protein Q4DY78 (UniProt accession number) from Trypanosoma cruzi is highly conserved in the related kinetoplastid pathogens Trypanosoma brucei and Leishmania major. Given the essentiality of its orthologue in T. brucei, the high sequence conservation with other trypanosomatid proteins, and the low sequence similarity with mammalian proteins, Q4DY78 is an attractive protein for structural characterization. Here, we solved the structure of Q4DY78 by solution NMR and evaluated its backbone dynamics. Q4DY78 is composed of five α -helices and a small, two-stranded antiparallel β-sheet. The backbone RMSD is 0.22 ± 0.05 Å for the representative ensemble of the 20 lowest-energy structures. Q4DY78 is overall rigid, except for N-terminal residues (V8 to I10), residues at loop 4 (K57 to G65) and residues at the C-terminus (F89 to F112). Q4DY78 has a short motif FPCAP that could potentially mediate interactions with the host cytoskeleton via interaction with EVH1 (Drosophila Enabled (Ena)/Vasodilator-stimulated phosphoprotein (VASP) homology 1) domains. Albeit Q4DY78 lacks calcium-binding motifs, its fold resembles that of eukaryotic calcium-binding proteins such as calcitracin, calmodulin, and polcacin Bet V4. We characterized this novel protein with a calcium binding fold without the capacity to bind calcium.
Collapse
Affiliation(s)
- Éverton Dias D'Andréa
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, sala 32, Rio de Janeiro, RJ 21941-902, Brazil
| | - Joren Sebastian Retel
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Anne Diehl
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie, FMP, Robert-Rössle-Straβe 10, Berlin 13125, Germany; Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, Berlin 14195, Germany
| | - José Ricardo Pires
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373 - Bloco E, sala 32, Rio de Janeiro, RJ 21941-902, Brazil.
| |
Collapse
|
2
|
Chamberlin A, Huether R, Machado AZ, Groden M, Liu HM, Upadhyay K, O V, Gomes NL, Lerario AM, Nishi MY, Costa EMF, Mendonca B, Domenice S, Velasco J, Loke J, Ostrer H. Mutations in MAP3K1 that cause 46,XY disorders of sex development disrupt distinct structural domains in the protein. Hum Mol Genet 2020; 28:1620-1628. [PMID: 30608580 DOI: 10.1093/hmg/ddz002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/19/2018] [Accepted: 12/31/2018] [Indexed: 02/07/2023] Open
Abstract
Missense mutations in the gene, MAP3K1, are a common cause of 46,XY gonadal dysgenesis, accounting for 15-20% of cases [Ostrer, 2014, Disorders of sex development (DSDs): an update. J. Clin. Endocrinol. Metab., 99, 1503-1509]. Functional studies demonstrated that all of these mutations cause a protein gain-of-function that alters co-factor binding and increases phosphorylation of the downstream MAP kinase pathway targets, MAPK11, MAP3K and MAPK1. This dysregulation of the MAP kinase pathway results in increased CTNNB1, increased expression of WNT4 and FOXL2 and decreased expression of SRY and SOX9. Unique and recurrent pathogenic mutations cluster in three semi-contiguous domains outside the kinase region of the protein, a newly identified N-terminal domain that shares homology with the Guanine Exchange Factor (residues Met164 to Glu231), a Plant HomeoDomain (residues Met442 to Trp495) and an ARMadillo repeat domain (residues Met566 to Glu862). Despite the presence of the mutation clusters and clinical data, there exists a dearth of mechanistic insights behind the development imbalance. In this paper, we use structural modeling and functional data of these mutations to understand alterations of the MAP3K1 protein and the effects on protein folding, binding and downstream target phosphorylation. We show that these mutations have differential effects on protein binding depending on the domains in which they occur. These mutations increase the binding of the RHOA, MAP3K4 and FRAT1 proteins and generally decrease the binding of RAC1. Thus, pathologies in MAP3K1 disrupt the balance between the pro-kinase activities of the RHOA and MAP3K4 binding partners and the inhibitory activity of RAC1.
Collapse
Affiliation(s)
| | | | - Aline Z Machado
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Michael Groden
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Kinnari Upadhyay
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vivian O
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nathalia L Gomes
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Antonio M Lerario
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mirian Y Nishi
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Elaine M F Costa
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Berenice Mendonca
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | - Sorahia Domenice
- Division of Endocrinology, Hormone and Molecular Genetics Laboratory (LIM), Hospital das Clinicas, University of Sao Paulo Medical School, Avenida Dr. Eneas de C Aguiar, andar Bloco, São Paulo, SP, Brazil
| | | | - Johnny Loke
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| |
Collapse
|