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PDBsum entry 2c38
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2c38

 

 

 

 

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Contents
Protein chains
(+ 6 more) 271 a.a. *
(+ 6 more) 241 a.a. *
Ligands
AMP-AMP-AMP-AMP ×7
Metals
_CL ×12
* Residue conservation analysis
PDB id:
2c38
Name: Hydrolase
Title: Rnase ph core of the archaeal exosome in complex with a5 RNA
Structure: Probable exosome complex exonuclease 2. Chain: a, c, e, g, i, k, m, o, q, s, u, w. Engineered: yes. Probable exosome complex exonuclease 1. Chain: b, d, f, h, j, l, n, p, r, t, v, x. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
3.10Å     R-factor:   0.276     R-free:   0.289
Authors: E.Lorentzen,E.Conti
Key ref:
E.Lorentzen and E.Conti (2005). Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol Cell, 20, 473-481. PubMed id: 16285928 DOI: 10.1016/j.molcel.2005.10.020
Date:
04-Oct-05     Release date:   23-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9UXC0  (RRP42_SULSO) -  Exosome complex component Rrp42 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		275 a.a.
271 a.a.
Protein chains
Pfam   ArchSchema ?
Q9UXC2  (RRP41_SULSO) -  Exosome complex component Rrp41 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Seq:
Struc: 		248 a.a.
241 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X: E.C.3.1.13.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.molcel.2005.10.020 Mol Cell 20:473-481 (2005)
PubMed id: 16285928  
 
 
Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core.
E.Lorentzen, E.Conti.
 
  ABSTRACT  
 
The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. View of the S. solfataricus Rrp41-Rrp42 Exosome Core Bound to a Short Single-Stranded RNA 		Figure 3.
Figure 3. Reaction Mechanism
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 20, 473-481) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20660080 C.C.Yang, Y.T.Wang, Y.Y.Hsiao, L.G.Doudeva, P.H.Kuo, S.Y.Chow, and H.S.Yuan (2010).
Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation.
  RNA, 16, 1748-1759.
PDB codes: 3hkm 3krn
20445227 C.L.Ng, D.G.Waterman, A.A.Antson, and M.Ortiz-Lombardía (2010).
Structure of the Methanothermobacter thermautotrophicus exosome RNase PH ring.
  Acta Crystallogr D Biol Crystallogr, 66, 522-528.
PDB code: 2wnr
20090900 C.Lu, F.Ding, and A.Ke (2010).
Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.
  PLoS One, 5, e8739.
PDB code: 3l7z
21072061 H.Malet, M.Topf, D.K.Clare, J.Ebert, F.Bonneau, J.Basquin, K.Drazkowska, R.Tomecki, A.Dziembowski, E.Conti, H.R.Saibil, and E.Lorentzen (2010).
RNA channelling by the eukaryotic exosome.
  EMBO Rep, 11, 936-942.  
20507607 J.S.Luz, C.R.Ramos, M.C.Santos, P.P.Coltri, F.L.Palhano, D.Foguel, N.I.Zanchin, and C.C.Oliveira (2010).
Identification of archaeal proteins that affect the exosome function in vitro.
  BMC Biochem, 11, 22.  
19955569 K.P.Callahan, and J.S.Butler (2010).
TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6.
  J Biol Chem, 285, 3540-3547.  
20627589 M.Zhou, and C.V.Robinson (2010).
When proteomics meets structural biology.
  Trends Biochem Sci, 35, 522-529.  
20301164 R.Tomecki, K.Drazkowska, and A.Dziembowski (2010).
Mechanisms of RNA degradation by the eukaryotic exosome.
  Chembiochem, 11, 938-945.  
20392821 S.Hartung, T.Niederberger, M.Hartung, A.Tresch, and K.P.Hopfner (2010).
Quantitative analysis of processive RNA degradation by the archaeal RNA exosome.
  Nucleic Acids Res, 38, 5166-5176.
PDB codes: 3m7n 3m85
19225159 A.C.Graham, D.L.Kiss, and E.D.Andrulis (2009).
Core exosome-independent roles for Rrp6 in cell cycle progression.
  Mol Biol Cell, 20, 2242-2253.  
19060898 D.Schaeffer, B.Tsanova, A.Barbas, F.P.Reis, E.G.Dastidar, M.Sanchez-Rotunno, C.M.Arraiano, and A.van Hoof (2009).
The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities.
  Nat Struct Mol Biol, 16, 56-62.  
19879841 F.Bonneau, J.Basquin, J.Ebert, E.Lorentzen, and E.Conti (2009).
The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation.
  Cell, 139, 547-559.
PDB code: 2wp8
19327365 S.Nurmohamed, B.Vaidialingam, A.J.Callaghan, and B.F.Luisi (2009).
Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly.
  J Mol Biol, 389, 17-33.
PDB codes: 3gcm 3gll 3gme 3h1c
18955140 E.Lorentzen, J.Basquin, and E.Conti (2008).
Structural organization of the RNA-degrading exosome.
  Curr Opin Struct Biol, 18, 709-713.  
18078842 H.Ibrahim, J.Wilusz, and C.J.Wilusz (2008).
RNA recognition by 3'-to-5' exonucleases: the substrate perspective.
  Biochim Biophys Acta, 1779, 256-265.  
19111177 J.C.Greimann, and C.D.Lima (2008).
Reconstitution of RNA exosomes from human and Saccharomyces cerevisiae cloning, expression, purification, and activity assays.
  Methods Enzymol, 448, 185-210.  
18786828 M.Schmid, and T.H.Jensen (2008).
The exosome: a multipurpose RNA-decay machine.
  Trends Biochem Sci, 33, 501-510.  
18397327 M.V.Falaleeva, H.V.Chetverina, V.I.Ugarov, E.A.Uzlova, and A.B.Chetverin (2008).
Factors influencing RNA degradation by Thermus thermophilus polynucleotide phosphorylase.
  FEBS J, 275, 2214-2226.  
18353775 M.V.Navarro, C.C.Oliveira, N.I.Zanchin, and B.G.Guimarães (2008).
Insights into the mechanism of progressive RNA degradation by the archaeal exosome.
  J Biol Chem, 283, 14120-14131.
PDB codes: 2pnz 2po0 2po1 2po2
18083836 V.Portnoy, G.Palnizky, S.Yehudai-Resheff, F.Glaser, and G.Schuster (2008).
Analysis of the human polynucleotide phosphorylase (PNPase) reveals differences in RNA binding and response to phosphate compared to its bacterial and chloroplast counterparts.
  RNA, 14, 297-309.  
18812438 Z.Shi, W.Z.Yang, S.Lin-Chao, K.F.Chak, and H.S.Yuan (2008).
Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation.
  RNA, 14, 2361-2371.
PDB codes: 3cdi 3cdj
17173052 A.Dziembowski, E.Lorentzen, E.Conti, and B.Séraphin (2007).
A single subunit, Dis3, is essentially responsible for yeast exosome core activity.
  Nat Struct Mol Biol, 14, 15-22.  
17159918 A.Oddone, E.Lorentzen, J.Basquin, A.Gasch, V.Rybin, E.Conti, and M.Sattler (2007).
Structural and biochemical characterization of the yeast exosome component Rrp40.
  EMBO Rep, 8, 63-69.
PDB code: 2ja9
17601780 C.M.Arraiano, J.Bamford, H.Brüssow, A.J.Carpousis, V.Pelicic, K.Pflüger, P.Polard, and J.Vogel (2007).
Recent advances in the expression, evolution, and dynamics of prokaryotic genomes.
  J Bacteriol, 189, 6093-6100.  
17380186 E.Lorentzen, A.Dziembowski, D.Lindner, B.Seraphin, and E.Conti (2007).
RNA channelling by the archaeal exosome.
  EMBO Rep, 8, 470-476.
PDB codes: 2je6 2jea 2jeb
17203066 E.Wahle (2007).
Wrong PH for RNA degradation.
  Nat Struct Mol Biol, 14, 5-7.  
17942686 H.W.Wang, J.Wang, F.Ding, K.Callahan, M.A.Bratkowski, J.S.Butler, E.Nogales, and A.Ke (2007).
Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing.
  Proc Natl Acad Sci U S A, 104, 16844-16849.  
17704127 J.A.Stead, J.L.Costello, M.J.Livingstone, and P.Mitchell (2007).
The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein.
  Nucleic Acids Res, 35, 5556-5567.  
17189683 J.A.Worrall, and B.F.Luisi (2007).
Information available at cut rates: structure and mechanism of ribonucleases.
  Curr Opin Struct Biol, 17, 128-137.  
17395456 K.M.Reinisch, and S.L.Wolin (2007).
Emerging themes in non-coding RNA quality control.
  Curr Opin Struct Biol, 17, 209-214.  
17464287 K.Sasaki, T.Ose, N.Okamoto, K.Maenaka, T.Tanaka, H.Masai, M.Saito, T.Shirai, and D.Kohda (2007).
Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA.
  EMBO J, 26, 2584-2593.  
17471261 S.Hartung, and K.P.Hopfner (2007).
The exosome, plugged.
  EMBO Rep, 8, 456-457.  
17514363 S.Lin-Chao, N.T.Chiou, and G.Schuster (2007).
The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines.
  J Biomed Sci, 14, 523-532.  
17603538 S.Vanacova, and R.Stefl (2007).
The exosome and RNA quality control in the nucleus.
  EMBO Rep, 8, 651-657.  
16407406 A.C.Graham, D.L.Kiss, and E.D.Andrulis (2006).
Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci.
  Mol Biol Cell, 17, 1399-1409.  
16713559 E.Lorentzen, and E.Conti (2006).
The exosome and the proteasome: nano-compartments for degradation.
  Cell, 125, 651-654.  
16893880 H.A.Vincent, and M.P.Deutscher (2006).
Substrate recognition and catalysis by the exoribonuclease RNase R.
  J Biol Chem, 281, 29769-29775.  
16829983 J.Houseley, J.LaCava, and D.Tollervey (2006).
RNA-quality control by the exosome.
  Nat Rev Mol Cell Biol, 7, 529-539.  
16968219 K.Büttner, K.Wenig, and K.P.Hopfner (2006).
The exosome: a macromolecular cage for controlled RNA degradation.
  Mol Microbiol, 61, 1372-1379.  
17078816 P.Walter, F.Klein, E.Lorentzen, A.Ilchmann, G.Klug, and E.Evguenieva-Hackenberg (2006).
Characterization of native and reconstituted exosome complexes from the hyperthermophilic archaeon Sulfolobus solfataricus.
  Mol Microbiol, 62, 1076-1089.  
17174896 Q.Liu, J.C.Greimann, and C.D.Lima (2006).
Reconstitution, activities, and structure of the eukaryotic RNA exosome.
  Cell, 127, 1223-1237.
PDB code: 2nn6
16882719 S.F.Midtgaard, J.Assenholt, A.T.Jonstrup, L.B.Van, T.H.Jensen, and D.E.Brodersen (2006).
Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain.
  Proc Natl Acad Sci U S A, 103, 11898-11903.
PDB codes: 2hbj 2hbk 2hbl 2hbm
17065466 V.Portnoy, and G.Schuster (2006).
RNA polyadenylation and degradation in different Archaea; roles of the exosome and RNase R.
  Nucleic Acids Res, 34, 5923-5931.  
16327773 A.K.Eggleston (2005).
Threaded for degradation.
  Nat Struct Mol Biol, 12, 1029.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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