PDBsum entry 2zh6

Transferase/RNA

PDB id: 2zh6

Contents

Protein chain

437 a.a. *

DNA/RNA

Ligands

SO4

ATP

Metals

_MG

Waters ×104

* Residue conservation analysis

PDB id:

2zh6

Name:

Transferase/RNA

Title:

Complex structure of afcca with trnaminidcu and atp

Structure:

tRNA (34-mer). Chain: b. Engineered: yes. Cca-adding enzyme. Chain: a. Synonym: tRNA nucleotidyltransferase, tRNA adenylyl-/cytidylyl- transferase, tRNA cca-pyrophosphorylase, tRNA-nt. Engineered: yes

Source:

Synthetic: yes. Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.233 R-free: 0.251

Authors:

Y.Toh,K.Tomita

Key ref:

Y.Toh et al. (2008). Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme. Embo J, 27, 1944-1952. PubMed id: 18583961 DOI: 10.1038/emboj.2008.124

Date:

01-Feb-08 Release date: 05-Aug-08

Protein chain

O28126  (CCA_ARCFU) -  CCA-adding enzyme from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: 437 a.a.

Struc: 437 a.a.

DNA/RNA chain

G-G-C-C-C-G-G-G-G-C-G-G-U-U-C-G-A-U-U-C-C-G-C-C-C-U-G-G-G-C-C-A-C-U 34 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.72 - Cca tRNA nucleotidyltransferase.
• Reaction: a tRNA precursor + 2 CTP + ATP = a tRNA with a 3' CCA end + 3 diphosphate

tRNA precursor + 2 × CTP (Bound ligand (Het Group name = ATP) corresponds exactly) + ATP = tRNA with a 3' CCA end + 3 × diphosphate

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

reference

DOI no: 10.1038/emboj.2008.124

Embo J 27:1944-1952 (2008)

PubMed id: 18583961

Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme.

Y.Toh, T.Numata, K.Watanabe, D.Takeshita, O.Nureki, K.Tomita.

ABSTRACT

CCA-adding enzyme builds the 3'-end CCA of tRNA without a nucleic acid template. The mechanism for the maintenance of fidelity during the CCA-adding reaction remains elusive. Here, we present almost a dozen complex structures of the class I CCA-adding enzyme and tRNA mini-helices (mini-D(73)N(74), mini-D(73)N(74)C(75) and mini-D(73)C(74)N(75); D(73) is a discriminator nucleotide and N is either A, G, or U). The mini-D(73)N(74) complexes adopt catalytically inactive open forms, and CTP shifts the enzymes to the active closed forms and allows N(74) to flip for CMP incorporation. In contrast, unlike the catalytically active closed form of the mini-D(73)C(74)C(75) complex, the mini-D(73)N(74)C(75) and mini-D(73)C(74)N(75) complexes adopt inactive open forms. Only the mini-D(73)C(74)U(75) accepts AMP to a similar extent as mini-D(73)C(74)C(75), and ATP shifts the enzyme to a closed, active form and allows U(75) to flip for AMP incorporation. These findings suggest that the 3'-region of RNA is proofread, after two nucleotide additions, in the closed, active form of the complex at the AMP incorporation stage. This proofreading is a prerequisite for the maintenance of fidelity for complete CCA synthesis.