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protein ligands metals links
Transferase PDB id
1uet
Jmol
Contents
Protein chain
429 a.a. *
Ligands
ACT
Metals
_CA ×3
_MG
Waters ×304
* Residue conservation analysis
PDB id:
1uet
Name: Transferase
Title: Divergent evolutions of trinucleotide polymerization reveale archaeal cca-adding enzyme structure
Structure: tRNA nucleotidyltransferase. Chain: a. Engineered: yes
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.198     R-free:   0.242
Authors: O.Nureki,Riken Structural Genomics/proteomics Initiative (Rs
Key ref: M.Okabe et al. (2003). Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure. Embo J, 22, 5918-5927. PubMed id: 14592988 DOI: 10.1093/emboj/cdg563
Date:
21-May-03     Release date:   02-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O28126  (CCA_ARCFU) -  CCA-adding enzyme
Seq:
Struc: 		437 a.a.
429 a.a.
Key:    PfamA 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
 + 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     nucleotide binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1093/emboj/cdg563 Embo J 22:5918-5927 (2003)
PubMed id: 14592988  
 
 
Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure.
M.Okabe, K.Tomita, R.Ishitani, R.Ishii, N.Takeuchi, F.Arisaka, O.Nureki, S.Yokoyama.
 
  ABSTRACT  
 
CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase], a template-independent RNA polymerase, adds the defined 'cytidine-cytidine-adenosine' sequence onto the 3' end of tRNA. The archaeal CCA-adding enzyme (class I) and eubacterial/eukaryotic CCA-adding enzyme (class II) show little amino acid sequence homology, but catalyze the same reaction in a defined fashion. Here, we present the crystal structures of the class I archaeal CCA-adding enzyme from Archaeoglobus fulgidus, and its complexes with CTP and ATP at 2.0, 2.0 and 2.7 A resolutions, respectively. The geometry of the catalytic carboxylates and the relative positions of CTP and ATP to a single catalytic site are well conserved in both classes of CCA-adding enzymes, whereas the overall architectures, except for the catalytic core, of the class I and class II CCA-adding enzymes are fundamentally different. Furthermore, the recognition mechanisms of substrate nucleotides and tRNA molecules are distinct between these two classes, suggesting that the catalytic domains of class I and class II enzymes share a common origin, and distinct substrate recognition domains have been appended to form the two presently divergent classes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  20101632 Y.M.Hou (2010).
CCA addition to tRNA: implications for tRNA quality control.
  IUBMB Life, 62, 251-260.  
20004168 M.Morar, K.Bhullar, D.W.Hughes, M.Junop, and G.D.Wright (2009).
Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
  Structure, 17, 1649-1659.
PDB codes: 3jyy 3jz0
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
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.  
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
17179213 H.D.Cho, C.L.Verlinde, and A.M.Weiner (2007).
Reengineering CCA-adding enzymes to function as (U,G)- or dCdCdA-adding enzymes or poly(C,A) and poly(U,G) polymerases.
  Proc Natl Acad Sci U S A, 104, 54-59.  
16455665 H.D.Cho, Y.Chen, G.Varani, and A.M.Weiner (2006).
A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation.
  J Biol Chem, 281, 9801-9811.  
17051158 K.Tomita, R.Ishitani, S.Fukai, and O.Nureki (2006).
Complete crystallographic analysis of the dynamics of CCA sequence addition.
  Nature, 443, 956-960.
PDB codes: 2dr5 2dr7 2dr8 2dr9 2dra 2drb 2dvi
16028221 C.Lehmann, S.Pullalarevu, W.Krajewski, M.A.Willis, A.Galkin, A.Howard, and O.Herzberg (2005).
Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase.
  Proteins, 60, 807-811.
PDB code: 1no5
15590678 H.D.Cho, C.L.Verlinde, and A.M.Weiner (2005).
Archaeal CCA-adding enzymes: central role of a highly conserved beta-turn motif in RNA polymerization without translocation.
  J Biol Chem, 280, 9555-9566.  
16281058 J.Deng, N.L.Ernst, S.Turley, K.D.Stuart, and W.G.Hol (2005).
Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei.
  EMBO J, 24, 4007-4017.
PDB codes: 2b4v 2b51 2b56
15498478 A.M.Weiner (2004).
tRNA maturation: RNA polymerization without a nucleic acid template.
  Curr Biol, 14, R883-R885.  
15146073 G.Martin, and W.Keller (2004).
Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases.
  RNA, 10, 899-906.  
15265870 H.D.Cho, and A.M.Weiner (2004).
A single catalytically active subunit in the multimeric Sulfolobus shibatae CCA-adding enzyme can carry out all three steps of CCA addition.
  J Biol Chem, 279, 40130-40136.  
15295603 K.Tomita, S.Fukai, R.Ishitani, T.Ueda, N.Takeuchi, D.G.Vassylyev, and O.Nureki (2004).
Structural basis for template-independent RNA polymerization.
  Nature, 430, 700-704.
PDB code: 1vfg
15295590 Y.Xiong, and T.A.Steitz (2004).
Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template.
  Nature, 430, 640-645.
PDB codes: 1sz1 1tfw 1tfy
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.