PDBsum entry 2v3c

Signaling protein

PDB id: 2v3c

Contents

Protein chains

87 a.a. *

404 a.a. *

DNA/RNA

Waters ×474

* Residue conservation analysis

PDB id:

2v3c

Name:

Signaling protein

Title:

Crystal structure of the srp54-srp19-7s.S srp RNA complex of m. Jannaschii

Structure:

Signal recognition particle 19 kda protein. Chain: a, b. Synonym: srp19. Engineered: yes. Signal recognition 54 kda protein. Chain: c, d. Fragment: residues 3-427. Synonym: srp54. Engineered: yes.

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 2190

Resolution:

2.50Å R-factor: 0.247 R-free: 0.294

Authors:

T.Hainzl,S.Huang,A.E.Sauer-Eriksson

Key ref:

T.Hainzl et al. (2007). Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle. Proc Natl Acad Sci U S A, 104, 14911-14916. PubMed id: 17846429 DOI: 10.1073/pnas.0702467104

Date:

15-Jun-07 Release date: 04-Sep-07

Protein chains

Q58440  (SRP19_METJA) -  Signal recognition particle 19 kDa protein from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 87 a.a.

Struc: 87 a.a.

Protein chains

Q57565  (SRP54_METJA) -  Signal recognition particle 54 kDa protein from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 451 a.a.

Struc: 404 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

G-G-C-G-G-U-G-G-G-G-G-A-G-C-A-U-C-U-C-C-U-G-U-A-G-G-G-G-A-G-A-U-G-U-A-A-C-C-C- 96 bases

G-G-C-G-G-U-G-G-G-G-G-A-G-C-A-U-C-U-C-C-U-G-U-A-G-G-G-G-A-G-A-U-G-U-A-A-C-C-C- 96 bases

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.?
• Enzyme class 2: Chains C, D: E.C.3.6.5.4 - signal-recognition-particle GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0702467104

Proc Natl Acad Sci U S A 104:14911-14916 (2007)

PubMed id: 17846429

Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle.

T.Hainzl, S.Huang, A.E.Sauer-Eriksson.

ABSTRACT

The signal-recognition particle (SRP) is a ubiquitous protein-RNA complex that targets proteins to cellular membranes for insertion or secretion. A key player in SRP-mediated protein targeting is the evolutionarily conserved core consisting of the SRP RNA and the multidomain protein SRP54. Communication between the SRP54 domains is critical for SRP function, where signal sequence binding at the M domain directs receptor binding at the GTPase domain (NG domain). These SRP activities are linked to domain rearrangements, for which the role of SRP RNA is not clear. In free SRP, a direct interaction of the GTPase domain with SRP RNA has been proposed but has never been structurally verified. In this study, we present the crystal structure at 2.5-A resolution of the SRP54-SRP19-SRP RNA complex of Methanococcus jannaschii SRP. The structure reveals an RNA-bound conformation of the SRP54 GTPase domain, in which the domain is spatially well separated from the signal peptide binding site. The association of both the N and G domains with SRP RNA in free SRP provides further structural evidence for the pivotal role of SRP RNA in the regulation of the SRP54 activity.

Selected figure(s)

Figure 3.
Fig. 3. SRP54 NG domain–RNA interactions. (A) The molecular surface of the SRP54 NG domain (Left) and 7S.S RNA (Right) are shaded to indicate the different accessibilities of the surface areas at each residue (Left) and nucleotide (Right) between the free and complexed forms. The red areas define protein–RNA contacts. The molecule to the right is rotated by 180° with respect to the molecule to the left. (B) Interaction between the G domain loop connecting G1 and G2 and the RNA minor groove of helix 5. The side chains of Arg-122 and Lys-126 bind to the phosphate oxygen of A186 and the 2'-OH atom of C187 in the RNA strand that switches from helix 6 to 8. The main-chain oxygen of Lys-126 is hydrogen-bonded to the 2'-OH of C188, and forms a water-mediated contact with the guanine base of G231, the base partner of C187 in the G–C pair immediately above the three-way junction. Furthermore, the side chain of Lys-130 interacts with the phosphate group of C233. RNA is colored in red, protein residues are colored in blue, and hydrogen bonds are colored in green.

Figure 4.
Fig. 4. Ribbon representation of the GM-linker structure. In S domain A, Ser-301 forms a hydrogen bond with the 2'-OH group of C221 in helix 8, and Leu-302, Ala-306, and Met-309 make hydrophobic interactions with Gly-67 and Leu-68 situated in the apical loop between N3 and N4 in the N domain. The NG domain is shown in blue, the RNA is shown in red, the M domain is shown in green, and the GM-linker is shown in orange. The GM-linker in S domain B is shown in gray. The side chain of Asp-311 in B is also shown. The overlay is based on the SRP54 M domains.

Figures were selected by an automated process.