Structure of the phylogenetically most conserved domain of SRP RNA

Schmitz, Uli; Behrens, Stephan; Freymann, Douglas; Lukavsky, Peter J.; Walter, Peter; James, Thomas Leroy

doi:10.1017/s1355838299991458

Cited by 62 publications

(81 citation statements)

References 28 publications

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“…We infer from the binding of a guanine nucleotide to the external site that any interaction between the 4.5 S RNA and the Ffh:FtsY NG heterodimer at that site requires that a nucleotide base be flipped out. Such configurations are relatively common, as, for example, in structures of the conserved motif IVof the 4.5 S RNA alone, 46 the SRP RNA complex with Ffh M domain, 47 the RNA complexes of the SRP Alu domain, 48 and DNA-editing complexes involved in repair and excision of 8-oxoguanine:adenine mispairs. 49,50 Previously, mutations of residues associated with the activation region, in particular Arg195, have been assayed in the context of the assembled SRP: FtsY complex 15 and found to exhibit deficiencies in GTPase activation.…”

Section: Discussionmentioning

confidence: 99%

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Focia

Gawronski-Salerno

Coon

et al. 2006

Journal of Molecular Biology

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The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement. We have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the activation region. We report here the structure of a complex of the SRP GTPases formed in the presence of GDP:AlF 4 . This complex accommodates the putative transition-state analog without undergoing significant change from the structure of the ground-state complex formed in the presence of the GTP analog GMPPCP. However, small shifts that do occur within the shared catalytic chamber may be functionally important. Remarkably, an external nucleotide interaction site was identified at the activation region, revealed by an unexpected contaminating GMP molecule bound adjacent to the catalytic chamber. This site exhibits conserved sequence and structural features that suggest a direct interaction with RNA plays a role in regulating the activity of the SRP targeting complex.

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Section: Discussionmentioning

confidence: 99%

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Focia

Gawronski-Salerno

Coon

et al. 2006

Journal of Molecular Biology

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“…Sequence and secondary structures of the two loops show strong similarities in all organisms, and they comprise the binding site for the SRP54 M domain. The structures of 4.5 S RNA and 4.5 S RNA bound to the M domain from Escherichia coli show the symmetric loop to be rigid in structure, whereas the asymmetric loop displays considerable flexibility and undergoes a dramatic structural rearrangement upon SRP54 binding (Schmitz et al 1999;Batey et al 2000;Jovine et al 2000). In the SRP54M-RNA complex structure, the asymmetric loop is held in an unusual conformation, in which the bases of the long strand are fully exposed on the outside of the RNA helix.…”

Section: Introductionmentioning

confidence: 99%

Structural insights into SRP RNA: An induced fit mechanism for SRP assembly

Hainzl

Huang²,

Sauer‐Eriksson³

2005

RNA

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Proper assembly of large protein-RNA complexes requires sequential binding of the proteins to the RNA. The signal recognition particle (SRP) is a multiprotein-RNA complex responsible for the cotranslational targeting of proteins to biological membranes. Here we describe the crystal structure at 2.6-Å resolution of the S-domain of SRP RNA from the archeon Methanococcus jannaschii. Comparison of this structure with the SRP19-bound form reveals the nature of the SRP19-induced conformational changes, which promote subsequent SRP54 attachment. These structural changes are initiated at the SRP19 binding site and transmitted through helix 6 to looped-out adenosines, which form tertiary RNA interaction with helix 8. Displacement of these adenosines enforces a conformational change of the asymmetric loop structure in helix 8. In free RNA, the three unpaired bases A195, C196, and C197 are directed toward the helical axis, whereas upon SRP19 binding the loop backbone inverts and the bases are splayed out in a conformation that resembles the SRP54-bound form. Nucleotides adjacent to the bulged nucleotides seem to be particularly important in the regulation of this loop transition. Binding of SRP19 to 7S RNA reveals an elegant mechanism of how protein-induced changes are directed through an RNA molecule and may relate to those regulating the assembly of other RNPs.

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“…The structure of an RNA fragment comprising domain IV of E. coli 4+5S RNA has been determined by NMR (Schmitz et al+, 1999a(Schmitz et al+, , 1999b)+ Genetic and biochemical analyses indicated that the conserved nucleotides present in the internal loop are important for Ffh binding (Wood et al+, 1992;Lentzen et al+, 1996)+ The crystal structure of the complex of domain IV RNA with an M domain fragment of Ffh shows that the protein interacts with both internal loops and that the structure of loop B in the complex differs from that of the free RNA (Batey et al+, 2000)+…”

Section: Introductionmentioning

confidence: 99%

Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY

Jagath

Matassova

Leeuw³

et al. 2001

RNA

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Binding of Escherichia coli signal recognition particle (SRP) to its receptor, FtsY, requires the presence of 4.5S RNA, although FtsY alone does not interact with 4.5S RNA. In this study, we report that the exchange of the GGAA tetraloop sequence in domain IV of 4.5S RNA for UUCG abolishes SRP-FtsY interaction, as determined by gel retardation and membrane targeting experiments, whereas replacements with other GNRA-type tetraloops have no effect. A number of other base exchanges in the tetraloop sequence have minor or intermediate inhibitory effects. Base pair disruptions in the stem adjacent to the tetraloop or replacement of the closing C-G base pair with G-C partially restored function of the otherwise inactive UUCG mutant. Chemical probing by hydroxyl radical cleavage of 4.5S RNA variants show that replacing GGAA with UUCG in the tetraloop sequence leads to structural changes both within the tetraloop and in the adjacent stem; the latter change is reversed upon reverting the C-G closing base pair to G-C. These results show that the SRP-FtsY interaction is strongly influenced by the structure of the tetraloop region of SRP RNA, in particular the tetraloop stem, and suggest that both SRP RNA and Ffh undergo mutual structural adaptation to form SRP that is functional in the interaction with the receptor, FtsY.

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Structure of the phylogenetically most conserved domain of SRP RNA

Abstract: RNA Structure of the phylogenetically most conserved domain of SRP

Cited by 62 publications

References 28 publications

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Structure of a GDP:AlF4 Complex of the SRP GTPases Ffh and FtsY, and Identification of a Peripheral Nucleotide Interaction Site

Structural insights into SRP RNA: An induced fit mechanism for SRP assembly

Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY

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