PDBsum entry 3aql

Transferase

PDB id: 3aql

Contents

Protein chains

388 a.a. *

Ligands

GOL ×2

Metals

_MG ×2

* Residue conservation analysis

PDB id:

3aql

Name:

Transferase

Title:

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.

Resolution:

3.00Å R-factor: 0.237 R-free: 0.251

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

Date:

09-Nov-10 Release date: 09-Feb-11

Protein chains

C9QS13  (C9QS13_ECOD1) -

Enzyme reactions

• Enzyme class: E.C.2.7.7.19 - polynucleotide adenylyltransferase.
• Reaction: RNA(n) + ATP = RNA(n)-3'-adenine ribonucleotide + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.

ABSTRACT

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.