PDBsum entry 3aqn

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
388 a.a. *
ATP ×2
_MG ×2
Waters ×6
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Complex structure of bacterial protein (apo form ii)
Structure: Poly(a) polymerase. Chain: a, b. Fragment: unp residues 17-431. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 536056. Strain: k12. Gene: ecdh1_3459. Expressed in: escherichia coli. Expression_system_taxid: 536056.
3.30Å     R-factor:   0.251     R-free:   0.275
Authors: Y.Toh,D.Takeshita,K.Tomita
Key ref: Y.Toh et al. (2011). Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases. Structure, 19, 232-243. PubMed id: 21300291
09-Nov-10     Release date:   09-Feb-11    
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Protein chains
Pfam   ArchSchema ?
C9QS13  (C9QS13_ECOD1) -  Poly(A) polymerase I
454 a.a.
388 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Polynucleotide adenylyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + RNA(n) = diphosphate + RNA(n+1)
Bound ligand (Het Group name = ATP)
corresponds exactly
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     RNA processing   5 terms 
  Biochemical function     nucleotide binding     6 terms  


Structure 19:232-243 (2011)
PubMed id: 21300291  
Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases.
Y.Toh, D.Takeshita, T.Nagaike, T.Numata, K.Tomita.
PolyA polymerase (PAP) adds a polyA tail onto the 3'-end of RNAs without a nucleic acid template, using adenosine-5'-triphosphate (ATP) as a substrate. The mechanism for the substrate selection by eubacterial PAP remains obscure. Structural and biochemical studies of Escherichia coli PAP (EcPAP) revealed that the shape and size of the nucleobase-interacting pocket of EcPAP are maintained by an intra-molecular hydrogen-network, making it suitable for the accommodation of only ATP, using a single amino acid, Arg(197). The pocket structure is sustained by interactions between the catalytic domain and the RNA-binding domain. EcPAP has a flexible basic C-terminal region that contributes to optimal RNA translocation for processive adenosine 5'-monophosphate (AMP) incorporations onto the 3'-end of RNAs. A comparison of the EcPAP structure with those of other template-independent RNA polymerases suggests that structural changes of domain(s) outside the conserved catalytic core domain altered the substrate specificities of the template-independent RNA polymerases.