PDBsum entry 1f5a

Transferase

PDB id: 1f5a

Contents

Protein chain

463 a.a. *

Ligands

3AT

3PO

Metals

_MN ×3

Waters ×170

* Residue conservation analysis

PDB id:

1f5a

Name:

Transferase

Title:

Crystal structure of mammalian poly(a) polymerase

Structure:

Poly(a) polymerase. Chain: a. Fragment: c-terminal deletion mutant missing residues 514-738. Engineered: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å R-factor: 0.219 R-free: 0.261

Authors:

G.Martin,W.Keller,S.Doublie

Key ref:

G.Martin et al. (2000). Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J, 19, 4193-4203. PubMed id: 10944102 DOI: 10.1093/emboj/19.16.4193

Date:

13-Jun-00 Release date: 13-Sep-00

Protein chain

P25500  (PAPOA_BOVIN) -  Poly(A) polymerase alpha from Bos taurus

Seq: 739 a.a.

Struc: 463 a.a.

Enzyme reactions

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

RNA(n) (Bound ligand (Het Group name = 3AT) matches with 96.77% similarity) + ATP = RNA(n)-3'-adenine ribonucleotide (Bound ligand (Het Group name = 3PO) matches with 69.23% similarity) + diphosphate

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

reference

DOI no: 10.1093/emboj/19.16.4193

EMBO J 19:4193-4203 (2000)

PubMed id: 10944102

Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.

G.Martin, W.Keller, S.Doublié.

ABSTRACT

In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. We have solved the crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolution. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.

Selected figure(s)

Figure 1.
Figure 1 (A) Ribbon diagram of the bovine PAP complex with 3'-dATP. The catalytic domain (residues 60–173) is shown in orange, the central domain in blue (residues 20–59 and 174–352) and the C-terminal RNA-binding domain in purple (residues 353–498). The 3'-dATP molecule bound in the active site is shown in magenta, and the three metals ions are shown as yellow spheres. Helices are designated with letters, -strands with numbers. (B) Stereo view of the PAP complex in the same orientation as in (A). Every 20 residues are labeled. Secondary structure elements were determined by Procheck (Laskowski et al., 1993). Figures 1, 3, 4 and 5 were generated with SETOR (Evans, 1993).

Figure 3.
Figure 3 PAP active site showing the major interacting residues. The secondary structure elements are color-coded as in Figure 1. Residues are shown in blue, except when they share structural homology with other proteins: orange (pol and KanNt), green (KanNt) and purple (T7 DNA polymerase). Hydrogen bonds are shown as dashed gray lines.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 4193-4203) copyright 2000.

Figures were selected by the author.