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PDBsum entry 2dra

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/RNA PDB id
2dra
Jmol
Contents
Protein chain
437 a.a. *
DNA/RNA
Ligands
SO4
ATP
Metals
_MG
Waters ×184
* Residue conservation analysis
PDB id:
2dra
Name: Transferase/RNA
Title: Complex structure of cca-adding enzyme with trnaminidcc and atp
Structure: tRNA (34-mer). Chain: b. Engineered: yes. Cca-adding enzyme. Chain: a. Synonym: tRNA nucleotidyltransferase, tRNA adenylyl- /cytidylyl- transferase, tRNA cca-pyrophosphorylase, tRNA- nt. Engineered: yes
Source: Synthetic: yes. Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.213     R-free:   0.261
Authors: K.Tomita,R.Ishitani,S.Fukai,O.Nureki
Key ref:
K.Tomita et al. (2006). Complete crystallographic analysis of the dynamics of CCA sequence addition. Nature, 443, 956-960. PubMed id: 17051158 DOI: 10.1038/nature05204
Date:
08-Jun-06     Release date:   14-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O28126  (CCA_ARCFU) -  CCA-adding enzyme
Seq:
Struc:
437 a.a.
437 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.72  - Cca tRNA nucleotidyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate
tRNA precursor
Bound ligand (Het Group name = ATP)
matches with 87.00% similarity
+ 2 × CTP
+ ATP
= tRNA with a 3' CCA end
+ 3 × diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     RNA repair   4 terms 
  Biochemical function     CTP:tRNA cytidylyltransferase activity     13 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature05204 Nature 443:956-960 (2006)
PubMed id: 17051158  
 
 
Complete crystallographic analysis of the dynamics of CCA sequence addition.
K.Tomita, R.Ishitani, S.Fukai, O.Nureki.
 
  ABSTRACT  
 
CCA-adding polymerase matures the essential 3'-CCA terminus of transfer RNA without any nucleic-acid template. However, it remains unclear how the correct nucleotide triphosphate is selected in each reaction step and how the polymerization is driven by the protein and RNA dynamics. Here we present complete sequential snapshots of six complex structures of CCA-adding enzyme and four distinct RNA substrates with and without CTP (cytosine triphosphate) or ATP (adenosine triphosphate). The CCA-lacking RNA stem extends by one base pair to force the discriminator nucleoside into the active-site pocket, and then tracks back after incorporation of the first cytosine monophosphate (CMP). Accommodation of the second CTP clamps the catalytic cleft, inducing a reorientation of the turn, which flips C74 to allow CMP to be accepted. In contrast, after the second CMP is added, the polymerase and RNA primer are locked in the closed state, which directs the subsequent A addition. Between the CTP- and ATP-binding stages, the side-chain conformation of Arg 224 changes markedly; this is controlled by the global motion of the enzyme and position of the primer terminus, and is likely to achieve the CTP/ATP discrimination, depending on the polymerization stage. Throughout the CCA-adding reaction, the enzyme tail domain firmly anchors the TPsiC-loop of the tRNA, which ensures accurate polymerization and termination.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Expansion and contraction of the primer RNA helix at the mini-D stage. a, Extended mini-helix structure at the mini-D stage. The simulated annealed omit maps (contoured at 3.5 ) for the indicated nucleosides are shown. b, Back-tracked mini-helix structure at the mini-DC. Other stages have the same standard helix structure.
Figure 3.
Figure 3: Active-site structure at each reaction stage. a, Mini-D stage (the simulated annealed omit maps contoured at 4 for G1 and A73 are shown). b, Mini-DC stage. c, Mini-DC + CTP stage. d, Mini-DCC stage. e, Mini-DCC + ATP stage. f, Mini-DCCA stage. g, Mature tRNA dissociation stage (PDB ID: 1SZ1)^14. The acceptor stem expansion at the first CCA-adding step can easily be seen by the fact that Asp 291 recognizes the 2'-OH group of C72 in the mini-D stage, but A73 in the other stages. The catalytic triad comprises Glu 59, Asp 61 and Asp 110. The hydrogen bonds are represented by dotted lines.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 443, 956-960) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21321236 M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, and K.S.Murakami (2011).
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
  Proc Natl Acad Sci U S A, 108, 3566-3571.
PDB codes: 3q0a 3q22 3q23 3q24
21292163 Y.Bai, S.K.Srivastava, J.H.Chang, J.L.Manley, and L.Tong (2011).
Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase.
  Mol Cell, 41, 311-320.
PDB code: 3pq1
20348137 A.Hoffmeier, H.Betat, A.Bluschke, R.Günther, S.Junghanns, H.J.Hofmann, and M.Mörl (2010).
Unusual evolution of a catalytic core element in CCA-adding enzymes.
  Nucleic Acids Res, 38, 4436-4447.  
21071662 B.Pan, Y.Xiong, and T.A.Steitz (2010).
How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA.
  Science, 330, 937-940.
PDB codes: 3ouy 3ov7 3ova 3ovb 3ovs
20155482 H.Betat, C.Rammelt, and M.Mörl (2010).
tRNA nucleotidyltransferases: ancient catalysts with an unusual mechanism of polymerization.
  Cell Mol Life Sci, 67, 1447-1463.  
19878676 I.U.Heinemann, D.Söll, and L.Randau (2010).
Transfer RNA processing in archaea: unusual pathways and enzymes.
  FEBS Lett, 584, 303-309.  
20717102 M.Blaise, M.Bailly, M.Frechin, M.A.Behrens, F.Fischer, C.L.Oliveira, H.D.Becker, J.S.Pedersen, S.Thirup, and D.Kern (2010).
Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.
  EMBO J, 29, 3118-3129.
PDB code: 3kfu
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
20696927 S.Hamill, S.L.Wolin, and K.M.Reinisch (2010).
Structure and function of the polymerase core of TRAMP, a RNA surveillance complex.
  Proc Natl Acad Sci U S A, 107, 15045-15050.
PDB code: 3nyb
  20101632 Y.M.Hou (2010).
CCA addition to tRNA: implications for tRNA quality control.
  IUBMB Life, 62, 251-260.  
19696158 S.Kim, C.Liu, K.Halkidis, H.B.Gamper, and Y.M.Hou (2009).
Distinct kinetic determinants for the stepwise CCA addition to tRNA.
  RNA, 15, 1827-1836.  
19745807 Y.Toh, D.Takeshita, T.Numata, S.Fukai, O.Nureki, and K.Tomita (2009).
Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme.
  EMBO J, 28, 3353-3365.
PDB codes: 3h37 3h38 3h39 3h3a
18495940 H.D.Cho, V.D.Sood, D.Baker, and A.M.Weiner (2008).
On the role of a conserved, potentially helix-breaking residue in the tRNA-binding alpha-helix of archaeal CCA-adding enzymes.
  RNA, 14, 1284-1289.  
18466919 M.Dupasquier, S.Kim, K.Halkidis, H.Gamper, and Y.M.Hou (2008).
tRNA integrity is a prerequisite for rapid CCA addition: implication for quality control.
  J Mol Biol, 379, 579-588.  
18836497 R.Giegé (2008).
Toward a more complete view of tRNA biology.
  Nat Struct Mol Biol, 15, 1007-1014.  
18302315 X.Shan, T.A.Russell, S.M.Paul, D.B.Kushner, and P.B.Joyce (2008).
Characterization of a temperature-sensitive mutation that impairs the function of yeast tRNA nucleotidyltransferase.
  Yeast, 25, 219-233.  
18583961 Y.Toh, T.Numata, K.Watanabe, D.Takeshita, O.Nureki, and K.Tomita (2008).
Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme.
  EMBO J, 27, 1944-1952.
PDB codes: 2zh1 2zh2 2zh3 2zh4 2zh5 2zh6 2zh7 2zh8 2zh9 2zha 2zhb
17872511 G.Martin, and W.Keller (2007).
RNA-specific ribonucleotidyl transferases.
  RNA, 13, 1834-1849.  
17580114 H.Li (2007).
Complexes of tRNA and maturation enzymes: shaping up for translation.
  Curr Opin Struct Biol, 17, 293-301.  
17704128 S.Muller, J.B.Fourmann, C.Loegler, B.Charpentier, and C.Branlant (2007).
Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Psi55-synthase and RNA-guided RNA:Psi-synthase activities.
  Nucleic Acids Res, 35, 5610-5624.  
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.