ISDA

Deposition Date 2022-10-31

Release Date 2023-01-25

Last Version Date 2024-06-19

Entry Detail

PDB ID:

8BHD

Keywords:

RNA BINDING PROTEIN

Title:

N-terminal domain of Plasmodium berghei glutamyl-tRNA synthetase (Tbxo4 derivative crystal structure)

Biological Source:

Source Organism:

Plasmodium berghei ANKA (Taxon ID: 5823)

Host Organism:

Escherichia coli BL21

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.17 Å

R-Value Free:

0.23

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Glutamate--tRNA ligase
Gene (Uniprot):PBANKA_1362000
Chain IDs:A, B, C, D, E
Chain Length:249
Number of Molecules:5
Biological Source:Plasmodium berghei ANKA

UniProt ID:A0A509AR09

Ligand Molecules

GOL

SO4

Primary Citation

Solution X-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes.

Jaramillo Ponce, J.R, Theobald-Dietrich, A, Benas, P, Paulus, C, Sauter, C, Frugier, M, Jaramillo Ponce, J.R, Kapps, D, Paulus, C, Chicher, J, Frugier, M, Afonine, P.V, Grosse-Kunstleve, R.W, Echols, N, Headd, J.J, Moriarty, N.W, Mustyakimov, M, Terwilliger, T.C, Urzhumtsev, A, Zwart, P.H, Adams, P.D, Liebschner, D, Afonine, P.V, Baker, M.L, Bunkoczi, G, Chen, V.B, Croll, T.I, Hintze, B, Hung, L.W, Jain, S, McCoy, A.J, Moriarty, N.W, Oeffner, R.D, Poon, B.K, Prisant, M.G, Read, R.J, Richardson, J.S, Richardson, D.C, Sammito, M.D, Sobolev, O.V, Stockwell, D.H, Terwilliger, T.C, Urzhumtsev, A.G, Videau, L.L, Williams, C.J, Adams, P.D, Emsley, P, Cowtan, K, Cowtan, K, Cowtan, K, Skubak, P, Waterreus, W.J, Pannu, N.S, Abrahams, J.P, Leslie, A.G, Murshudov, G.N, Skubak, P, Lebedev, A.A, Pannu, N.S, Steiner, R.A, Nicholls, R.A, Winn, M.D, Long, F, Vagin, A.A, Schneider, T.R, Sheldrick, G.M, Sheldrick, G.M, Skubak, P, Pannu, N.S, Kabsch, W, Kabsch, W, Oscarsson, M, Beteva, A, Flot, D, Gordon, E, Guijarro, M, Leonard, G, McSweeney, S, Monaco, S, Mueller-Dieckmann, C, Nanao, M, Nurizzo, D, Popov, A.N, von Stetten, D, Svensson, O, Rey-Bakaikoa, V, Chado, I, Chavas, L.M.G, Gadea, L, Gourhant, P, Isabet, T, Legrand, P, Savko, M, Sirigu, S, Shepard, W, Thompson, A, Mueller, U, Nan, J, Eguiraun, M, Bolmsten, F, Nardella, A, Milan-Otero, A, Thunnissen, M, Hellmig, M, Kastner, A, Schmuckermaier, L, Gerlach, M, Feiler, C, Weiss, M.S, Bowler, M.W, Gobbo, A, Papp, G, Sinoir, J, McCarthy, A.A, Karpics, I, Nikolova, M, Bourenkov, G, Schneider, T, Andreu, J, Cuni, G, Juanhuix, J, Boer, R, Fogh, R, Keller, P, Flensburg, C, Paciorek, W, Vonrhein, C, Bricogne, G, de Sanctis, D, Coati, A, Chavas, L.M.G, Fontaine, P, Foos, N, Guimaraes, B, Gourhant, P, Legrand, P, Itie, J.P, Fertey, P, Shepard, W, Isabet, T, Sirigu, S, Solari, P.L, Thiaudiere, D, Thompson, A, Engilberge, S, Riobe, F, Di Pietro, S, Lassalle, L, Coquelle, N, Arnaud, C.A, Pitrat, D, Mulatier, J.C, Madern, D, Breyton, C, Maury, O, Girard, E.Show

Protein Sci. 32 e4564 e4564 (2023)

PMID: 36606712 DOI: 10.1002/pro.4564

Abstact

tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl-tRNA synthetases (aaRS), the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases. In eukaryotes, such multi-aaRSs complexes (MSC) regulate the moonlighting activities of aaRSs. In Plasmodium, tRip and the three aaRSs all contain an N-terminal GST-like domain involved in the assembly of two independent complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS) with a 2:2:2 stoichiometry and in which the association of the GST-like domains of tRip and ERS (tRip-N:ERS-N) is central. In this study, the crystal structure of the N-terminal GST-like domain of ERS was solved and made possible further investigation of the solution architecture of the Q- and M-complexes by small-angle x-ray scattering (SAXS). This strategy relied on the engineering of a tRip-N-ERS-N chimeric protein to study the structural scaffold of both Plasmodium MSCs and confirm the unique homodimerization pattern of tRip in solution. The biological impact of these structural arrangements is discussed.

Legend

Protein

Chemical

Disease

Primary Citation of related structures