PDBsum entry 2qi2

Cell cycle

PDB id: 2qi2

Contents

Protein chain

312 a.a. *

Waters ×17

* Residue conservation analysis

PDB id:

2qi2

Name:

Cell cycle

Title:

Crystal structure of the thermoplasma acidophilum pelota protein

Structure:

Cell division protein pelota related protein. Chain: a. Synonym: pelota. Engineered: yes

Source:

Thermoplasma acidophilum. Organism_taxid: 2303. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.90Å R-factor: 0.214 R-free: 0.263

Authors:

H.H.Lee,Y.S.Kim,K.H.Kim,I.H.Heo,S.K.Kim,O.Kim,S.W.Suh

Key ref:

H.H.Lee et al. (2007). Structural and functional insights into dom34, a key component of no-go mRNA decay. Mol Cell, 27, 938-950. PubMed id: 17889667 DOI: 10.1016/j.molcel.2007.07.019

Date:

03-Jul-07 Release date: 09-Oct-07

Protein chain

Q9HJ74  (PELO_THEAC) -  Protein pelota homolog from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

Seq: 339 a.a.

Struc: 312 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.-.-

DOI no: 10.1016/j.molcel.2007.07.019

Mol Cell 27:938-950 (2007)

PubMed id: 17889667

Structural and functional insights into dom34, a key component of no-go mRNA decay.

H.H.Lee, Y.S.Kim, K.H.Kim, I.Heo, S.K.Kim, O.Kim, H.K.Kim, J.Y.Yoon, H.S.Kim, d.o. .J.Kim, S.J.Lee, H.J.Yoon, S.J.Kim, B.G.Lee, H.K.Song, V.N.Kim, C.M.Park, S.W.Suh.

ABSTRACT

The yeast protein Dom34 is a key component of no-go decay, by which mRNAs with translational stalls are endonucleolytically cleaved and subsequently degraded. However, the identity of the endoribonuclease is unknown. Homologs of Dom34, called Pelota, are broadly conserved in eukaryotes and archaea. To gain insights into the structure and function of Dom34/Pelota, we have determined the structure of Pelota from Thermoplasma acidophilum (Ta Pelota) and investigated the ribonuclease activity of Dom34/Pelota. The structure of Ta Pelota is tripartite, and its domain 1 has the RNA-binding Sm fold. We have discovered that Ta Pelota has a ribonuclease activity and that its domain 1 is sufficient for the catalytic activity. We also demonstrate that domain 1 of Dom34 has an endoribonuclease activity against defined RNA substrates containing a stem loop, which supports a direct catalytic role of yeast Dom34 in no-go mRNA decay.

Selected figure(s)

Figure 3.
Figure 3. Structural Comparison of Ta Pelota and the Sm Protein from P. aerophilum
(A) Superposition of domain 1 of Ta Pelota (magenta tube) and the P. aerophilum Sm protein (orange tube) (PDB code 1I8F; Mura et al. [2001]). The conserved Asn46 and Arg69 of the P. aerophilum Sm protein, termed RNA-binding knuckles (Khusial et al., 2005), are shown.
(B) Heptamer structure of the P. aerophilum Sm protein.
(C) Schematic diagram comparing domain structures of Ta Pelota and eRF1.
(D) Stereo 2F[o] − F[c] electron density map around the Pro197-Gly198-Phe199 sequence of Ta Pelota.

Figure 5.
Figure 5. Putative Active Site and Surface View of Ta Pelota
(A) Stereo ribbon diagram around the putative active site. Three conserved acidic residues in motif I are shown.
(B) Two different views of the electrostatic potential at the molecular surface of Ta Pelota (blue, positive; red, negative). They are roughly 90° apart. The location of conserved acidic residues in motif I is indicated by the yellow dotted ellipse. The green dotted ellipse on the right panel indicates the positively charged surface patch next to sequence motif I.

The above figures are reprinted by permission from Cell Press: Mol Cell (2007, 27, 938-950) copyright 2007.

Figures were selected by an automated process.