PDBsum entry 2gje

Translation/RNA

PDB id

2gje

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Contents

			Protein chains

					145 a.a.


					147 a.a.

			DNA/RNA

			Waters ×1

PDB id:

2gje

Links

Name:

Translation/RNA

Title:

Structure of a guiderna-binding protein complex bound to a grna

Structure:

Guide RNA 40-mer. Chain: r. Engineered: yes. RNA tetramer. Chain: s. Engineered: yes. Mitochondrial RNA-binding protein 2. Chain: a. Synonym: mrp2, guide RNA-binding protein.

Source:

Synthetic: yes. Trypanosoma brucei. Organism_taxid: 185431. Strain: treu927. Gene: mrp1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: mrp2.

Biol. unit:

Octamer (from PQS)

Resolution:

3.37Å

R-factor:

0.282

R-free:

0.300

Authors:

M.A.Schumacher,E.Karamooz,A.Zikova,L.Trantirek,J.Lukes

Key ref:

M.A.Schumacher et al. (2006). Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism. Cell, 126, 701-711. PubMed id: 16923390 DOI: 10.1016/j.cell.2006.06.047

Date:

30-Mar-06

Release date:

05-Sep-06

PROCHECK

	Headers

	References

Protein chain

Q952G2 (Q952G2_9TRYP) - Guide RNA binding protein gBP25 from Trypanosoma brucei

Seq: Struc:					224 a.a. 145 a.a.

Protein chain

P90629 (P90629_9TRYP) - GBP21 from Trypanosoma brucei

Seq: Struc:					206 a.a. 147 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

		U-A-A-A-U-A-A-C-C-U-G-U-A 13 bases
		U-A-G-U-G 5 bases

DOI no: 10.1016/j.cell.2006.06.047	Cell 126:701-711 (2006)
PubMed id: 16923390

Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism.
M.A.Schumacher, E.Karamooz, A.Zíková, L.Trantírek, J.Lukes.

ABSTRACT

The mitochondrial RNA binding proteins MRP1 and MRP2 form a heteromeric complex that functions in kinetoplastid RNA editing. In this process, MRP1/MRP2 serves as a matchmaker by binding to guide RNAs and facilitating their hybridization with cognate preedited mRNAs. To understand the mechanism by which this complex performs RNA matchmaking, we determined structures of Trypanosoma brucei apoMRP1/MRP2 and an MRP1/MRP2-gRNA complex. The structures show that MRP1/MRP2 is a heterotetramer and, despite little sequence homology, each MRP subunit exhibits the same "Whirly" transcription-factor fold. The gRNA molecule binds to the highly basic beta sheet surface of the MRP complex via nonspecific, electrostatic contacts. Strikingly, while the gRNA stem/loop II base is anchored to the basic surface, stem/loop I (the anchor sequence) is unfolded and its bases exposed to solvent. Thus, MRP1/MRP2 acts as an RNA matchmaker by stabilizing the RNA molecule in an unfolded conformation suitable for RNA-RNA hybridization.

Selected figure(s)



	Figure 1. Figure 1. Structure of the MRP1/MRP2 Complex		Figure 2. Figure 2. MRP1 and MRP2 Have “Whirly” Transcription-Factor Folds and Form a Heterotetramer

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21321231

F.Li, J.Herrera, S.Zhou, D.A.Maslov, and L.Simpson (2011).
Trypanosome REH1 is an RNA helicase involved with the 3'-5' polarity of multiple gRNA-guided uridine insertion/deletion RNA editing.

Proc Natl Acad Sci U S A, 108, 3542-3547.

20018860

A.Schnaufer, M.Wu, Y.J.Park, T.Nakai, J.Deng, R.Proff, W.G.Hol, and K.D.Stuart (2010).
A protein-protein interaction map of trypanosome ~20S editosomes.

J Biol Chem, 285, 5282-5295.

20808932

L.Reifur, L.E.Yu, J.Cruz-Reyes, M.Vanhartesvelt, and D.J.Koslowsky (2010).
The impact of mRNA structure on guide RNA targeting in kinetoplastid RNA editing.

PLoS One, 5, e12235.

19945343

L.Simpson, R.Aphasizhev, J.Lukes, and J.Cruz-Reyes (2010).
Guide to the nomenclature of kinetoplastid RNA editing: a proposal.

Protist, 161, 2-6.

20392699

M.Sprehe, J.C.Fisk, S.M.McEvoy, L.K.Read, and M.A.Schumacher (2010).
Structure of the Trypanosoma brucei p22 protein, a cytochrome oxidase subunit II-specific RNA-editing accessory factor.

J Biol Chem, 285, 18899-18908.

PDB code:

3jv1

20713467

S.Kala, and R.Salavati (2010).
OB-fold domain of KREPA4 mediates high-affinity interaction with guide RNA and possesses annealing activity.

RNA, 16, 1951-1967.

20181740

S.Martin-Tumasz, N.J.Reiter, D.A.Brow, and S.E.Butcher (2010).
Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24.

RNA, 16, 792-804.

PDB code:

2kh9

19846792

A.Graebsch, S.Roche, and D.Niessing (2009).
X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface.

Proc Natl Acad Sci U S A, 106, 18521-18526.

PDB code:

3k44

19228586

H.Hashimi, Z.Cicová, L.Novotná, Y.Z.Wen, and J.Lukes (2009).
Kinetoplastid guide RNA biogenesis is dependent on subunits of the mitochondrial RNA binding complex 1 and mitochondrial RNA polymerase.

RNA, 15, 588-599.

19620277

J.C.Fisk, V.Presnyak, M.L.Ammerman, and L.K.Read (2009).
Distinct and overlapping functions of MRP1/2 and RBP16 in mitochondrial RNA metabolism.

Mol Cell Biol, 29, 5214-5225.

19197238

M.M.Golas, C.Böhm, B.Sander, K.Effenberger, M.Brecht, H.Stark, and H.U.Göringer (2009).
Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo.

EMBO J, 28, 766-778.

19190092

M.Niemann, H.Kaibel, E.Schlüter, K.Weitzel, M.Brecht, and H.U.Göringer (2009).
Kinetoplastid RNA editing involves a 3' nucleotidyl phosphatase activity.

Nucleic Acids Res, 37, 1897-1906.

19096045

N.Acestor, A.K.Panigrahi, J.Carnes, A.Zíková, and K.D.Stuart (2009).
The MRB1 complex functions in kinetoplastid RNA processing.

RNA, 15, 277-286.

19567872

Q.Xu, B.A.Traag, J.Willemse, D.McMullan, M.D.Miller, M.A.Elsliger, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, D.Carlton, C.Chen, H.J.Chiu, M.Chruszcz, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, D.Ernst, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, S.K.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, D.Marciano, W.Minor, A.M.Mommaas, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, S.Wang, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson, and G.P.van Wezel (2009).
Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes.

J Biol Chem, 284, 25268-25279.

PDB code:

3cm1

18423020

A.Maréchal, J.S.Parent, M.Sabar, F.Véronneau-Lafortune, C.Abou-Rached, and N.Brisson (2008).
Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function.

BMC Plant Biol, 8, 42.

18295767

A.Zíková, J.Kopecná, M.A.Schumacher, K.Stuart, L.Trantírek, and J.Lukes (2008).
Structure and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei.

Int J Parasitol, 38, 901-912.

18369185

H.Hashimi, A.Zíková, A.K.Panigrahi, K.D.Stuart, and J.Lukes (2008).
TbRGG1, an essential protein involved in kinetoplastid RNA metabolism that is associated with a novel multiprotein complex.

RNA, 14, 970-980.

18441050

J.A.Law, S.F.O'Hearn, and B.Sollner-Webb (2008).
Trypanosoma brucei RNA editing protein TbMP42 (band VI) is crucial for the endonucleolytic cleavages but not the subsequent steps of U-deletion and U-insertion.

RNA, 14, 1187-1200.

18676978

J.Prikryl, K.P.Watkins, G.Friso, K.J.van Wijk, and A.Barkan (2008).
A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis.

Nucleic Acids Res, 36, 5152-5165.

18951088

J.Weng, I.Aphasizheva, R.D.Etheridge, L.Huang, X.Wang, A.M.Falick, and R.Aphasizhev (2008).
Guide RNA-binding complex from mitochondria of trypanosomatids.

Mol Cell, 32, 198-209.

18772247

L.Reifur, and D.J.Koslowsky (2008).
Trypanosoma brucei ATPase subunit 6 mRNA bound to gA6-14 forms a conserved three-helical structure.

RNA, 14, 2195-2211.

18441045

M.L.Ammerman, J.C.Fisk, and L.K.Read (2008).
gRNA/pre-mRNA annealing and RNA chaperone activities of RBP16.

RNA, 14, 1069-1080.

18603593

M.Niemann, M.Brecht, E.Schlüter, K.Weitzel, M.Zacharias, and H.U.Göringer (2008).
TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism.

Nucleic Acids Res, 36, 4465-4473.

18243097

O.Barabas, D.R.Ronning, C.Guynet, A.B.Hickman, B.Ton-Hoang, M.Chandler, and F.Dyda (2008).
Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection.

Cell, 132, 208-220.

PDB codes:

2vhg 2vic 2vih 2vju 2vjv

17320109

E.Bae, N.J.Reiter, C.A.Bingman, S.S.Kwan, D.Lee, G.N.Phillips, S.E.Butcher, and D.A.Brow (2007).
Structure and interactions of the first three RNA recognition motifs of splicing factor prp24.

J Mol Biol, 367, 1447-1458.

PDB codes:

2ghp 2go9

17287292

M.J.Madej, J.D.Alfonzo, and A.Hüttenhofer (2007).
Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae.

Nucleic Acids Res, 35, 1544-1554.

17369311

V.K.Babbarwal, M.Fleck, N.L.Ernst, A.Schnaufer, and K.Stuart (2007).
An essential role of KREPB4 in RNA editing and structural integrity of the editosome in Trypanosoma brucei.

RNA, 13, 737-744.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.