PDBsum entry 3l7z

Hydrolase/RNA binding protein

PDB id: 3l7z

Contents

Protein chains

251 a.a. *

232 a.a. *

222 a.a. *

215 a.a. *

270 a.a. *

206 a.a. *

Ligands

SO4 ×3

* Residue conservation analysis

PDB id:

3l7z

Name:

Hydrolase/RNA binding protein

Title:

Crystal structure of the s. Solfataricus archaeal exosome

Structure:

Probable exosome complex exonuclease 2. Chain: a, d, g. Engineered: yes. Probable exosome complex exonuclease 1. Chain: b, e, h. Engineered: yes. Probable exosome complex RNA-binding protein 1. Chain: c, f, i. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Gene: c20_023, rrp41/42/4, sso0732. Expressed in: escherichia coli. Expression_system_taxid: 469008. Gene: sso0735. Gene: c20_026, sso0736.

Resolution:

2.41Å R-factor: 0.266 R-free: 0.289

Authors:

C.Lu,F.Ding,A.Ke

Key ref:

C.Lu et al. (2010). Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. Plos One, 5, e8739. PubMed id: 20090900

Date:

29-Dec-09 Release date: 23-Jun-10

Protein chains

Q9UXC0  (RRP42_SULSO) -  Exosome complex component Rrp42 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 275 a.a.

Struc: 251 a.a.

Protein chains

Q9UXC2  (RRP41_SULSO) -  Exosome complex component Rrp41 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 248 a.a.

Struc: 232 a.a.

Protein chain

Q9UXC4  (RRP4_SACS2) -  Exosome complex component Rrp4 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 249 a.a.

Struc: 222 a.a.

Protein chain

Q9UXC4  (RRP4_SACS2) -  Exosome complex component Rrp4 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 249 a.a.

Struc: 215 a.a.

Protein chain

Q9UXC0  (RRP42_SULSO) -  Exosome complex component Rrp42 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 275 a.a.

Struc: 270 a.a.*

Protein chain

Q9UXC4  (RRP4_SACS2) -  Exosome complex component Rrp4 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 249 a.a.

Struc: 206 a.a.

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

Enzyme reactions

• Enzyme class: Chains A, B, D, E, G, H: E.C.3.1.13.- - ?????

Plos One 5:e8739 (2010)

PubMed id: 20090900

Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

C.Lu, F.Ding, A.Ke.

ABSTRACT

BACKGROUND: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. METHODOLOGY/PRINCIPAL FINDINGS: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. CONCLUSION/SIGNIFICANCE: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.