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PDBsum entry 1a79

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protein ligands metals Protein-protein interface(s) links
Endonuclease PDB id
1a79
Jmol
Contents
Protein chains
171 a.a. *
Ligands
SO4 ×2
Metals
_AU ×4
Waters ×53
* Residue conservation analysis
PDB id:
1a79
Name: Endonuclease
Title: Crystal structure of the tRNA splicing endonuclease from methanococcus jannaschii
Structure: tRNA endonuclease. Chain: a, b, c, d. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: blr (de3).
Biol. unit: Tetramer (from PQS)
Resolution:
2.28Å     R-factor:   0.200     R-free:   0.267
Authors: H.Li,C.R.Trotta,J.N.Abelson
Key ref:
H.Li et al. (1998). Crystal structure and evolution of a transfer RNA splicing enzyme. Science, 280, 279-284. PubMed id: 9535656 DOI: 10.1126/science.280.5361.279
Date:
23-Mar-98     Release date:   01-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58819  (ENDA_METJA) -  tRNA-splicing endonuclease
Seq:
Struc:
179 a.a.
171 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.6.1.16  - tRNA-intron lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   5 terms 
  Biochemical function     nucleic acid binding     4 terms  

 

 
DOI no: 10.1126/science.280.5361.279 Science 280:279-284 (1998)
PubMed id: 9535656  
 
 
Crystal structure and evolution of a transfer RNA splicing enzyme.
H.Li, C.R.Trotta, J.Abelson.
 
  ABSTRACT  
 
The splicing of transfer RNA precursors is similar in Eucarya and Archaea. In both kingdoms an endonuclease recognizes the splice sites and releases the intron, but the mechanism of splice site recognition is different in each kingdom. The crystal structure of the endonuclease from the archaeon Methanococcus jannaschii was determined to a resolution of 2.3 angstroms. The structure indicates that the cleavage reaction is similar to that of ribonuclease A and the arrangement of the active sites is conserved between the archaeal and eucaryal enzymes. These results suggest an evolutionary pathway for splice site recognition.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. (A) Ribbon representation of one subunit of M. jannaschii endonuclease obtained with the RIBBONS program (20). The^ proposed catalytic triad residues are within 7 Å of each other^ and are shown in red ball-and-stick models (see text). The electron^ density in the averaged F[o] map is contoured at 5 and is drawn^ only near the putative catalytic triad. (B) Subunit arrangement^ and interactions in the M. jannaschii endonuclease. Each subunit^ is represented by a distinct color and a label. The tetramer is^ viewed along the true twofold axis relating the A1-A2 and B1-B2^ dimers. The main chain hydrogen bonds formed between 9 and 9 ^and between loops L8 and L8 for isologous dimers are drawn as^thin lines. Side chains of the hydrophobic residues enclosed at^ the dimer interface are shown as blue ball-and-stick models. The^ heterologous interaction between subunits A1 and B2 (or B1 and^ A2) through the acidic loops L10 and L8 are highlighted by dotted^ surfaces.
Figure 3.
Fig. 3. (A) Sequence and secondary structure of HIV TAR RNA (PDB code 1arj) used to model M. jannaschii pre-tRNA minimum substrate. (B) A symmetry operation around the twofold axis as indicated^ is applied to coordinates of the TAR RNA nuclear magnetic resonance^ structure to obtain a structural model for the second three-base^ bulge and the stem extension (boxed region). The corresponding splice sites on the final model are indicated by arrows. (C) Modeled complex of M. jannaschii endonuclease with RNA substrate^ obtained by manually aligning the phosphate backbone of the 4-bp helix with the positively charged surface between subunits A1^ and B1. This view is perpendicular to that of Fig. 2B. Only subunits A1 and B1, which are proposed to participate in the cleavage reaction, are shown. The proposed catalytic triad residues are shown in magenta. The phosphodiester bonds at the splice sites on RNA are^ depicted in blue and fit nearly perfectly with the putative sulfate^ density shown by blue dots. The distance from the center of the^ catalytic triad to the surface where RNA binds is about 7 Å.
 
  The above figures are reprinted by permission from the AAAs: Science (1998, 280, 279-284) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19878676 I.U.Heinemann, D.Söll, and L.Randau (2010).
Transfer RNA processing in archaea: unusual pathways and enzymes.
  FEBS Lett, 584, 303-309.  
20430862 K.Fujishima, J.Sugahara, M.Tomita, and A.Kanai (2010).
Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain.
  Mol Biol Evol, 27, 2233-2243.  
19578064 M.Mitchell, S.Xue, R.Erdman, L.Randau, D.Söll, and H.Li (2009).
Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease.
  Nucleic Acids Res, 37, 5793-5802.
PDB codes: 3iey 3if0
19625490 N.T.Uyen, S.Y.Park, J.W.Choi, H.J.Lee, K.Nishi, and J.S.Kim (2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
  Nucleic Acids Res, 37, 6960-6969.
PDB code: 3h1t
19515941 S.Yoshinari, T.Shiba, D.K.Inaoka, T.Itoh, G.Kurisu, S.Harada, K.Kita, and Y.Watanabe (2009).
Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease.
  Nucleic Acids Res, 37, 4787-4798.
PDB code: 2zyz
18474864 A.M.Anderson, and J.P.Staley (2008).
Long-distance splicing.
  Proc Natl Acad Sci U S A, 105, 6793-6794.  
18648070 A.Ramirez, S.Shuman, and B.Schwer (2008).
Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo.
  RNA, 14, 1737-1745.  
18094118 B.Schwer, A.Aronova, A.Ramirez, P.Braun, and S.Shuman (2008).
Mammalian 2',3' cyclic nucleotide phosphodiesterase (CNP) can function as a tRNA splicing enzyme in vivo.
  RNA, 14, 204-210.  
18458335 G.Di Segni, S.Gastaldi, and G.P.Tocchini-Valentini (2008).
Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells.
  Proc Natl Acad Sci U S A, 105, 6864-6869.  
18832079 J.Sugahara, K.Kikuta, K.Fujishima, N.Yachie, M.Tomita, and A.Kanai (2008).
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales.
  Mol Biol Evol, 25, 2709-2716.  
18286179 K.Fujishima, J.Sugahara, M.Tomita, and A.Kanai (2008).
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.
  PLoS ONE, 3, e1622.  
18552771 L.Randau, and D.Söll (2008).
Transfer RNA genes in pieces.
  EMBO Rep, 9, 623-628.  
17472738 C.Hammann, and E.Westhof (2007).
Searching genomes for ribozymes and riboswitches.
  Genome Biol, 8, 210.  
17636125 G.D.Tocchini-Valentini, P.Fruscoloni, and G.P.Tocchini-Valentini (2007).
The dawn of dominance by the mature domain in tRNA splicing.
  Proc Natl Acad Sci U S A, 104, 12300-12305.  
17166513 J.Song, and J.L.Markley (2007).
Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold.
  J Mol Biol, 366, 155-164.
PDB code: 2gw6
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.  
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.  
17227452 T.Taguchi, S.Okamoto, A.Lezhava, A.Li, K.Ochi, Y.Ebizuka, and K.Ichinose (2007).
Possible involvement of ActVI-ORFA in transcriptional regulation of actVI tailoring-step genes for actinorhodin biosynthesis.
  FEMS Microbiol Lett, 269, 234-239.  
17352735 T.Yoshihisa, C.Ohshima, K.Yunoki-Esaki, and T.Endo (2007).
Cytoplasmic splicing of tRNA in Saccharomyces cerevisiae.
  Genes Cells, 12, 285-297.  
17827289 Y.K.Kim, K.Mizutani, K.H.Rhee, K.H.Nam, W.H.Lee, E.H.Lee, E.E.Kim, S.Y.Park, and K.Y.Hwang (2007).
Structural and mutational analysis of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728: catalytic mechanism of tRNA intron-splicing endonucleases.
  J Bacteriol, 189, 8339-8346.
PDB codes: 2ohc 2ohe
16710424 C.R.Trotta, S.V.Paushkin, M.Patel, H.Li, and S.W.Peltz (2006).
Cleavage of pre-tRNAs by the splicing endonuclease requires a composite active site.
  Nature, 441, 375-377.  
16790566 S.Blanga-Kanfi, M.Amitsur, A.Azem, and G.Kaufmann (2006).
PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase.
  Nucleic Acids Res, 34, 3209-3219.  
15985153 D.J.Rigden (2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
  BMC Struct Biol, 5, 9.  
15937113 G.D.Tocchini-Valentini, P.Fruscoloni, and G.P.Tocchini-Valentini (2005).
Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization.
  Proc Natl Acad Sci U S A, 102, 8933-8938.  
16221764 G.D.Tocchini-Valentini, P.Fruscoloni, and G.P.Tocchini-Valentini (2005).
Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea.
  Proc Natl Acad Sci U S A, 102, 15418-15422.  
16330750 L.Randau, K.Calvin, M.Hall, J.Yuan, M.Podar, H.Li, and D.Söll (2005).
The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves.
  Proc Natl Acad Sci U S A, 102, 17934-17939.  
15653639 M.Englert, and H.Beier (2005).
Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins.
  Nucleic Acids Res, 33, 388-399.  
15720711 M.Feder, and J.M.Bujnicki (2005).
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
  BMC Genomics, 6, 21.  
15987815 M.H.Renalier, N.Joseph, C.Gaspin, P.Thebault, and A.Mougin (2005).
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.
  RNA, 11, 1051-1063.  
15109492 S.V.Paushkin, M.Patel, B.S.Furia, S.W.Peltz, and C.R.Trotta (2004).
Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation.
  Cell, 117, 311-321.  
14993668 Y.Zhang, and H.Li (2004).
Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2.
  Acta Crystallogr D Biol Crystallogr, 60, 447-452.
PDB codes: 1r0v 1r11
14624007 C.Marck, and H.Grosjean (2003).
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications.
  RNA, 9, 1516-1531.  
12881427 E.J.Tran, X.Zhang, and E.S.Maxwell (2003).
Efficient RNA 2'-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C'/D' RNPs.
  EMBO J, 22, 3930-3940.  
12598892 M.Aittaleb, R.Rashid, Q.Chen, J.R.Palmer, C.J.Daniels, and H.Li (2003).
Structure and function of archaeal box C/D sRNP core proteins.
  Nat Struct Biol, 10, 256-263.
PDB code: 1nt2
12592006 S.R.Salgia, S.K.Singh, P.Gurha, and R.Gupta (2003).
Two reactions of Haloferax volcanii RNA splicing enzymes: joining of exons and circularization of introns.
  RNA, 9, 319-330.  
12925762 T.Yoshihisa, K.Yunoki-Esaki, C.Ohshima, N.Tanaka, and T.Endo (2003).
Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria.
  Mol Biol Cell, 14, 3266-3279.  
12490712 A.Jäger, R.Samorski, F.Pfeifer, and G.Klug (2002).
Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase.
  Nucleic Acids Res, 30, 5436-5443.  
11809414 C.Conrad, and R.Rauhut (2002).
Ribonuclease III: new sense from nuisance.
  Int J Biochem Cell Biol, 34, 116-129.  
12403461 C.Marck, and H.Grosjean (2002).
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.
  RNA, 8, 1189-1232.  
12358432 E.Bini, V.Dikshit, K.Dirksen, M.Drozda, and P.Blum (2002).
Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus.
  RNA, 8, 1129-1136.  
11929612 J.M.Bujnicki, and L.Rychlewski (2002).
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
  BMC Bioinformatics, 3, 10.  
  11897024 L.M.Iyer, E.V.Koonin, and L.Aravind (2002).
Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.
  Genome Biol, 3, RESEARCH0012.  
11917006 V.Anantharaman, E.V.Koonin, and L.Aravind (2002).
Comparative genomics and evolution of proteins involved in RNA metabolism.
  Nucleic Acids Res, 30, 1427-1464.  
11344334 J.M.Bujnicki, and L.Rychlewski (2001).
Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.
  Protein Sci, 10, 656-660.  
11266363 P.Fruscoloni, M.I.Baldi, and G.P.Tocchini-Valentini (2001).
Cleavage of non-tRNA substrates by eukaryal tRNA splicing endonucleases.
  EMBO Rep, 2, 217-221.  
11406387 S.A.Teichmann, A.G.Murzin, and C.Chothia (2001).
Determination of protein function, evolution and interactions by structural genomics.
  Curr Opin Struct Biol, 11, 354-363.  
11685244 X.Yang, T.Gérczei, L.T.Glover, and C.C.Correll (2001).
Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
  Nat Struct Biol, 8, 968-973.
PDB codes: 1jbr 1jbs 1jbt
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
10917597 L.Zofallova, Y.Guo, and R.Gupta (2000).
Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract.
  RNA, 6, 1019-1030.  
10745015 T.Hermann, and D.J.Patel (2000).
RNA bulges as architectural and recognition motifs.
  Structure, 8, R47-R54.  
  10430568 A.G.Russell, H.Ebhardt, and P.P.Dennis (1999).
Substrate requirements for a novel archaeal endonuclease that cleaves within the 5' external transcribed spacer of Sulfolobus acidocaldarius precursor rRNA.
  Genetics, 152, 1373-1385.  
10371039 A.W.Nicholson (1999).
Function, mechanism and regulation of bacterial ribonucleases.
  FEMS Microbiol Rev, 23, 371-390.  
10872451 P.B.Moore (1999).
Structural motifs in RNA.
  Annu Rev Biochem, 68, 287-300.  
10400475 S.Cusack (1999).
RNA-protein complexes.
  Curr Opin Struct Biol, 9, 66-73.  
10578109 T.H.Waterman (1999).
The evolutionary challenges of extreme environments (Part 1).
  J Exp Zool, 285, 326-359.  
9660971 J.L.Diener, and P.B.Moore (1998).
Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif.
  Mol Cell, 1, 883-894.
PDB codes: 1a9l 1u3k 2a9l
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.