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PDBsum entry 2j7o

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protein metals links
Hydrolase PDB id
2j7o
Jmol
Contents
Protein chain
935 a.a. *
Metals
_MG
* Residue conservation analysis
PDB id:
2j7o
Name: Hydrolase
Title: Structure of the rnai polymerase from neurospora crassa
Structure: RNA dependent RNA polymerase. Chain: a. Fragment: residues 381-1402. Synonym: hypothetical protein ncu075341. Engineered: yes
Source: Neurospora crassa. Organism_taxid: 5141. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
3.50Å     R-factor:   0.353     R-free:   0.359
Authors: P.S.Salgado,M.R.L.Koivunen,E.V.Makeyev,D.H.Bamford, D.I.Stuart,J.M.Grimes
Key ref: P.S.Salgado et al. (2006). The structure of an RNAi polymerase links RNA silencing and transcription. PLoS Biol, 4, e434. PubMed id: 17147473
Date:
13-Oct-06     Release date:   13-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Y7G6  (Q9Y7G6_NEUCS) -  RNA-dependent RNA polymerase (Fragment)
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1402 a.a.
935 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA-directed RNA polymerase activity     1 term  

 

 
PLoS Biol 4:e434 (2006)
PubMed id: 17147473  
 
 
The structure of an RNAi polymerase links RNA silencing and transcription.
P.S.Salgado, M.R.Koivunen, E.V.Makeyev, D.H.Bamford, D.I.Stuart, J.M.Grimes.
 
  ABSTRACT  
 
RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant single-stranded RNA. We report the 2.3-A resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, and find that it forms a relatively compact dimeric molecule, each subunit of which comprises several domains with, at its core, a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription. This evolutionary link between the two enzyme types suggests that aspects of RNA silencing in some organisms may recapitulate transcription/replication pathways functioning in the ancient RNA-based world.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21233849 F.Werner, and D.Grohmann (2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
  Nat Rev Microbiol, 9, 85-98.  
21294682 Y.Maida, and K.Masutomi (2011).
RNA-dependent RNA polymerases in RNA silencing.
  Biol Chem, 392, 299-304.  
20360047 G.Ruprich-Robert, and P.Thuriaux (2010).
Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases.
  Nucleic Acids Res, 38, 4559-4569.  
  20957187 H.C.Lee, A.P.Aalto, Q.Yang, S.S.Chang, G.Huang, D.Fisher, J.Cha, M.M.Poranen, D.H.Bamford, and Y.Liu (2010).
The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring replication protein A and a DNA helicase.
  PLoS Biol, 8, 0.  
20680389 L.Li, S.S.Chang, and Y.Liu (2010).
RNA interference pathways in filamentous fungi.
  Cell Mol Life Sci, 67, 3849-3863.  
19444217 H.C.Lee, S.S.Chang, S.Choudhary, A.P.Aalto, M.Maiti, D.H.Bamford, and Y.Liu (2009).
qiRNA is a new type of small interfering RNA induced by DNA damage.
  Nature, 459, 274-277.  
19239877 P.A.Sharp (2009).
The centrality of RNA.
  Cell, 136, 577-580.  
19701182 Y.Maida, M.Yasukawa, M.Furuuchi, T.Lassmann, R.Possemato, N.Okamoto, V.Kasim, Y.Hayashizaki, W.C.Hahn, and K.Masutomi (2009).
An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA.
  Nature, 461, 230-235.  
  18268843 K.K.Ng, J.J.Arnold, and C.E.Cameron (2008).
Structure-function relationships among RNA-dependent RNA polymerases.
  Curr Top Microbiol Immunol, 320, 137-156.  
18715673 S.A.Shabalina, and E.V.Koonin (2008).
Origins and evolution of eukaryotic RNA interference.
  Trends Ecol Evol, 23, 578-587.  
17496045 A.E.Wallin, A.Salmi, and R.Tuma (2007).
Step length measurement--theory and simulation for tethered bead constant-force single molecule assay.
  Biophys J, 93, 795-805.  
18004386 E.Lehmann, F.Brueckner, and P.Cramer (2007).
Molecular basis of RNA-dependent RNA polymerase II activity.
  Nature, 450, 445-449.
PDB codes: 2r92 2r93
18007599 K.Aoki, H.Moriguchi, T.Yoshioka, K.Okawa, and H.Tabara (2007).
In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans.
  EMBO J, 26, 5007-5019.  
17921288 S.Stolyar, Q.He, M.P.Joachimiak, Z.He, Z.K.Yang, S.E.Borglin, D.C.Joyner, K.Huang, E.Alm, T.C.Hazen, J.Zhou, J.D.Wall, A.P.Arkin, and D.A.Stahl (2007).
Response of Desulfovibrio vulgaris to alkaline stress.
  J Bacteriol, 189, 8944-8952.  
17395524 V.Fulci, and G.Macino (2007).
Quelling: post-transcriptional gene silencing guided by small RNAs in Neurospora crassa.
  Curr Opin Microbiol, 10, 199-203.  
17580115 W.R.Taylor (2007).
Evolutionary transitions in protein fold space.
  Curr Opin Struct Biol, 17, 354-361.  
17015657 E.S.Charlson, J.N.Werner, and R.Misra (2006).
Differential effects of yfgL mutation on Escherichia coli outer membrane proteins and lipopolysaccharide.
  J Bacteriol, 188, 7186-7194.  
17015661 M.I.Hutchings, H.J.Hong, E.Leibovitz, I.C.Sutcliffe, and M.J.Buttner (2006).
The sigma(E) cell envelope stress response of Streptomyces coelicolor is influenced by a novel lipoprotein, CseA.
  J Bacteriol, 188, 7222-7229.  
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.