PDBsum entry 3wfs

Transferase/RNA

PDB id: 3wfs

Contents

Protein chains

436 a.a.

DNA/RNA

Ligands

SO4 ×4

PDB id:

3wfs

Name:

Transferase/RNA

Title:

tRNA processing enzyme complex 3

Structure:

RNA (74-mer). Chain: a, b. Engineered: yes. Poly a polymerase. Chain: c, d. Engineered: yes

Source:

Synthetic: yes. Thermotoga maritima msb8. Organism_taxid: 243274. Synthetic construct, aquifex aeolicus (strain vf5). Organism_taxid: 32630, 224324. Strain: vf5. Gene: pcnb2. Expressed in: escherichia coli.

Resolution:

3.31Å R-factor: 0.231 R-free: 0.276

Authors:

S.Yamashita,D.Takeshita,K.Tomita

Key ref:

S.Yamashita et al. (2014). Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase. Structure, 22, 315-325. PubMed id: 24389024 DOI: 10.1016/j.str.2013.12.002

Date:

23-Jul-13 Release date: 01-Jan-14

Protein chains

O67911  (O67911_AQUAE) -  CC-adding tRNA nucleotidyltransferase from Aquifex aeolicus (strain VF5)

Seq: 512 a.a.

Struc: 436 a.a.*

* PDB and UniProt seqs differ at 33 residue positions (black crosses)

DNA/RNA chains

G-G-C-C-A-G-G-U-A-G-C-U-C-A-G-U-U-G-G-U-A-G-A-G-C-A-C-U-G-G-A-C-U-G-A-A-A-A-U- 74 bases

G-G-C-C-A-G-G-U-A-G-C-U-C-A-G-U-U-G-G-U-A-G-A-G-C-A-C-U-G-G-A-C-U-G-A-A-A-A-U- 74 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.- - ?????

DOI no: 10.1016/j.str.2013.12.002

Structure 22:315-325 (2014)

PubMed id: 24389024

Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase.

S.Yamashita, D.Takeshita, K.Tomita.

ABSTRACT

The 3'-terminal CCA (CCA-3' at positions 74-76) of tRNA is synthesized by CCA-adding enzyme using CTP and ATP as substrates, without a nucleic acid template. In Aquifex aeolicus, CC-adding and A-adding enzymes collaboratively synthesize the CCA-3'. The mechanism of CCA-3' synthesis by these two enzymes remained obscure. We now present crystal structures representing CC addition onto tRNA by A. aeolicus CC-adding enzyme. After C₇₄ addition in an enclosed active pocket and pyrophosphate release, the tRNA translocates and rotates relative to the enzyme, and C₇₅ addition occurs in the same active pocket as C₇₄ addition. At both the C₇₄-adding and C₇₅-adding stages, CTP is selected by Watson-Crick-like hydrogen bonds between the cytosine of CTP and conserved Asp and Arg residues in the pocket. After C₇₄C₇₅ addition and pyrophosphate release, the tRNA translocates further and drops off the enzyme, and the CC-adding enzyme terminates RNA polymerization.