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PDBsum entry 2ba1
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protein metals Protein-protein interface(s) links
RNA binding protein PDB id
2ba1

 

 

 

 

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Contents
Protein chains
179 a.a. *
245 a.a. *
247 a.a. *
Metals
_ZN ×3
Waters ×83
* Residue conservation analysis
PDB id:
2ba1
Name: RNA binding protein
Title: Archaeal exosome core
Structure: Archaeal exosome RNA binding protein csl4. Chain: a, c, b. Engineered: yes. Archaeal exosome complex exonuclease rrp41. Chain: e, d, f. Engineered: yes. Archaeal exosome complex exonuclease rrp42. Chain: h, g, i. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Nonamer (from PQS)
Resolution:
2.70Å     R-factor:   0.224     R-free:   0.275
Authors: K.P.Hopfner,K.Buttner,K.Wenig
Key ref:
K.Büttner et al. (2005). Structural framework for the mechanism of archaeal exosomes in RNA processing. Mol Cell, 20, 461-471. PubMed id: 16285927 DOI: 10.1016/j.molcel.2005.10.018
Date:
13-Oct-05     Release date:   22-Nov-05    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
O30033  (CSL4_ARCFU) -  Exosome complex component Csl4 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		179 a.a.
179 a.a.
Protein chains
Pfam   ArchSchema ?
O29757  (RRP41_ARCFU) -  Exosome complex component Rrp41 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		258 a.a.
245 a.a.
Protein chains
Pfam   ArchSchema ?
O29756  (RRP42_ARCFU) -  Exosome complex component Rrp42 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
Seq:
Struc: 		259 a.a.
247 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, C, B: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: Chains E, D, F, H, G, I: E.C.3.1.13.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
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.

 

 
DOI no: 10.1016/j.molcel.2005.10.018 Mol Cell 20:461-471 (2005)
PubMed id: 16285927  
 
 
Structural framework for the mechanism of archaeal exosomes in RNA processing.
K.Büttner, K.Wenig, K.P.Hopfner.
 
  ABSTRACT  
 
Exosomes emerge as central 3'-->5' RNA processing and degradation machineries in eukaryotes and archaea. We determined crystal structures of two 230 kDa nine subunit archaeal exosome isoforms. Both exosome isoforms contain a hexameric ring of RNase phosphorolytic (PH) domain subunits with a central chamber. Tungstate soaks identified three phosphorolytic active sites in this processing chamber. A trimer of Csl4 or Rrp4 subunits forms a multidomain macromolecular interaction surface on the RNase-PH domain ring with central S1 domains and peripheral KH and zinc-ribbon domains. Structural and mutational analyses suggest that the S1 domains and a subsequent neck in the RNase-PH domain ring form an RNA entry pore to the processing chamber that only allows access of unstructured RNA. This structural framework can mechanistically unify observed features of exosomes, including processive degradation of unstructured RNA, the requirement for regulatory factors to degrade structured RNA, and left-over tails in rRNA trimming.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Phosphorolytic Active Sites 		Figure 6.
Figure 6. Proposed Mechanism for Core Exosomes
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 20, 461-471) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
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
20185544 D.L.Kiss, and E.D.Andrulis (2010).
Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits.
  RNA, 16, 781-791.  
21082788 G.Lee, S.Hartung, K.P.Hopfner, and T.Ha (2010).
Reversible and Controllable Nanolocomotion of an RNA-Processing Machinery.
  Nano Lett, 10, 5123-5130.  
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.  
  21129205 M.Uzan, and E.S.Miller (2010).
Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation.
  Virol J, 7, 360.  
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
18245385 D.Hasenöhrl, T.Lombo, V.Kaberdin, P.Londei, and U.Bläsi (2008).
Translation initiation factor a/eIF2(-gamma) counteracts 5' to 3' mRNA decay in the archaeon Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 105, 2146-2150.  
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.  
18940861 K.P.Callahan, and J.S.Butler (2008).
Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p.
  Nucleic Acids Res, 36, 6645-6655.  
18786828 M.Schmid, and T.H.Jensen (2008).
The exosome: a multipurpose RNA-decay machine.
  Trends Biochem Sci, 33, 501-510.  
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
18493045 S.L.Zimmer, Z.Fei, and D.B.Stern (2008).
Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features.
  Genetics, 179, 125-136.  
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
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
18075576 C.V.Robinson, A.Sali, and W.Baumeister (2007).
The molecular sociology of the cell.
  Nature, 450, 973-982.  
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.  
17412707 G.Schilders, E.van Dijk, and G.J.Pruijn (2007).
C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing.
  Nucleic Acids Res, 35, 2564-2572.  
17280603 G.Schilders, R.Raijmakers, K.C.Malmegrim, L.Vande Walle, X.Saelens, W.Vree Egberts, W.J.van Venrooij, P.Vandenabeele, and G.J.Pruijn (2007).
Caspase-mediated cleavage of the exosome subunit PM/Scl-75 during apoptosis.
  Arthritis Res Ther, 9, R12.  
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.  
17174977 K.Calvin, and H.Li (2007).
Achieving specific RNA cleavage activity by an inactive splicing endonuclease subunit through engineered oligomerization.
  J Mol Biol, 366, 642-649.  
17395456 K.M.Reinisch, and S.L.Wolin (2007).
Emerging themes in non-coding RNA quality control.
  Curr Opin Struct Biol, 17, 209-214.  
17471261 S.Hartung, and K.P.Hopfner (2007).
The exosome, plugged.
  EMBO Rep, 8, 456-457.  
17644597 S.Hundt, A.Zaigler, C.Lange, J.Soppa, and G.Klug (2007).
Global analysis of mRNA decay in Halobacterium salinarum NRC-1 at single-gene resolution using DNA microarrays.
  J Bacteriol, 189, 6936-6944.  
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.  
16955096 D.Grossman, and A.van Hoof (2006).
RNase II structure completes group portrait of 3' exoribonucleases.
  Nat Struct Mol Biol, 13, 760-761.  
16713559 E.Lorentzen, and E.Conti (2006).
The exosome and the proteasome: nano-compartments for degradation.
  Cell, 125, 651-654.  
16729021 H.Hernández, A.Dziembowski, T.Taverner, B.Séraphin, and C.V.Robinson (2006).
Subunit architecture of multimeric complexes isolated directly from cells.
  EMBO Rep, 7, 605-610.  
17053084 J.Bove, C.L.Hord, and M.A.Mullen (2006).
The blossoming of RNA biology: Novel insights from plant systems.
  RNA, 12, 2035-2046.  
16829983 J.Houseley, J.LaCava, and D.Tollervey (2006).
RNA-quality control by the exosome.
  Nat Rev Mol Cell Biol, 7, 529-539.  
16912217 J.R.Anderson, D.Mukherjee, K.Muthukumaraswamy, K.C.Moraes, C.J.Wilusz, and J.Wilusz (2006).
Sequence-specific RNA binding mediated by the RNase PH domain of components of the exosome.
  RNA, 12, 1810-1816.  
16968219 K.Büttner, K.Wenig, and K.P.Hopfner (2006).
The exosome: a macromolecular cage for controlled RNA degradation.
  Mol Microbiol, 61, 1372-1379.  
16766188 M.J.Marcaida, M.A.DePristo, V.Chandran, A.J.Carpousis, and B.F.Luisi (2006).
The RNA degradosome: life in the fast lane of adaptive molecular evolution.
  Trends Biochem Sci, 31, 359-365.  
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
17130171 S.Durand, G.Richard, M.Bisaglia, S.Laalami, F.Bontems, and M.Uzan (2006).
Activation of RegB endoribonuclease by S1 ribosomal protein requires an 11 nt conserved sequence.
  Nucleic Acids Res, 34, 6549-6560.  
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.  
16996291 Y.Zuo, H.A.Vincent, J.Zhang, Y.Wang, M.P.Deutscher, and A.Malhotra (2006).
Structural basis for processivity and single-strand specificity of RNase II.
  Mol Cell, 24, 149-156.
PDB code: 2id0
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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