PDBsum entry 2ja9

RNA binding protein

PDB id: 2ja9

Contents

Protein chain

175 a.a. *

Waters ×96

* Residue conservation analysis

PDB id:

2ja9

Name:

RNA binding protein

Title:

Structure of the n-terminal deletion of yeast exosome component rrp40

Structure:

Exosome complex exonuclease rrp40. Chain: a. Fragment: residues 62-236. Synonym: rrp40, ribosomal RNA-processing protein 40. Engineered: yes

Source:

Saccharomyces cerevisiae. Bakers' yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.190 R-free: 0.206

Authors:

A.Oddone,E.Lorentzen,J.Basquin,A.Gasch,V.Rybin,E.Conti,M.Sattler

Key ref:

A.Oddone et al. (2007). Structural and biochemical characterization of the yeast exosome component Rrp40. EMBO Rep, 8, 63-69. PubMed id: 17159918 DOI: 10.1038/sj.embor.7400856

Date:

24-Nov-06 Release date: 13-Dec-06

Protein chain

Q08285  (RRP40_YEAST) -  Exosome complex component RRP40 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 240 a.a.

Struc: 175 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.13.- - ?????

DOI no: 10.1038/sj.embor.7400856

EMBO Rep 8:63-69 (2007)

PubMed id: 17159918

Structural and biochemical characterization of the yeast exosome component Rrp40.

A.Oddone, E.Lorentzen, J.Basquin, A.Gasch, V.Rybin, E.Conti, M.Sattler.

ABSTRACT

The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome.

Selected figure(s)

Figure 2.
Figure 2 Structure of Saccharomyces cerevisiae Rrp40 N. (A) Crystal structure of S. cerevisiae Rrp40 N (comprising residues 63–236). The S1 domain, the KH domain and the conserved GxNG motif are indicated. (B) Superposition of the structures of Rrp40 N (magenta) and of AfRrp4 (orange; Büttner et al, 2005). The two different GxxG sequence motifs present in AfRrp4 are indicated. (C) Detailed view of the GxNG loop connecting 7 and 8 in the ScRrp40 KH domain. Hydrogen bonds formed by Asn 191 with residues of the S1 domain are indicated by dotted lines. (D) View of the S1–KH domain interface. Conserved hydrophobic side chains, which stabilize the domain interface, are shown in black. Af, Archaeoglobus fulgidus.

Figure 3.
Figure 3 Charge, conservation and interaction surfaces of Rrp40 N. Molecular surface representations of Rrp40: left, the same view as that depicted in Fig 2; right, rotated by 180° along a vertical axis. (A) Molecular surfaces are coloured blue and red according to positive and negative electrostatic potential, respectively. (B) The degree of sequence conservation among Rrp40 orthologues is mapped on the surface representation. Dark or light green indicates residues that are fully or partially conserved in Rrp40 orthologues, respectively (compare with Fig 1). (C) The conserved residues of the 3– 4 loop and the residues affected on addition of Mn^2+ are shown in magenta and cyan, respectively. (D) Model of Rrp40 N in the context of the exosome, obtained by replacing one of the Rrp4 subunits in the structure of the Archaeoglobus fulgidus (Af) exosome by Rrp40 N. The conserved residues in the 3– 4 loop of the S1 domain and those affected by the addition of Mn^2+ are shown in magenta and cyan, respectively. The AfRrp41 and AfRrp42 subunits are shown in blue and green, respectively, and the two AfRrp4 subunits are shown in orange. Ribbon and surface representations were generated with PyMOL (http://pymol.sourceforge.net).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO Rep (2007, 8, 63-69) copyright 2007.

Figures were selected by an automated process.