PDBsum entry 4i2c

Transferase/DNA

PDB id: 4i2c

Contents

Protein chain

359 a.a.

DNA/RNA

Ligands

APC

Metals

_MN ×2

_NA

Waters ×349

PDB id:

4i2c

Name:

Transferase/DNA

Title:

Ternary complex of mouse tdt with ssdna and ampcpp

Structure:

DNA nucleotidylexotransferase. Chain: a. Fragment: see remark 999. Synonym: terminal addition enzyme, terminal deoxynucleotidyltransferase, tdt, terminal transferase. Engineered: yes. 5'-d( Ap Ap Ap Ap A)-3'. Chain: c. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: dntt, tdt. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.10Å R-factor: 0.183 R-free: 0.217

Authors:

J.Gouge,M.Delarue

Key ref:

J.Gouge et al. (2013). Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism. J Mol Biol, 425, 4334-4352. PubMed id: 23856622 DOI: 10.1016/j.jmb.2013.07.009

Date:

21-Nov-12 Release date: 24-Jul-13

Protein chain

P09838  (TDT_MOUSE) -  DNA nucleotidylexotransferase from Mus musculus

Seq: 510 a.a.

Struc: 359 a.a.

DNA/RNA chain

A-A-A 3 bases

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.31 - Dna nucleotidylexotransferase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.1.11.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1016/j.jmb.2013.07.009

J Mol Biol 425:4334-4352 (2013)

PubMed id: 23856622

Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism.

J.Gouge, S.Rosario, F.Romain, P.Beguin, M.Delarue.

ABSTRACT

Terminal deoxynucleotidyltransferase (Tdt) is a non-templated eukaryotic DNA polymerase of the polX family that is responsible for the random addition of nucleotides at the V(D)J junctions of immunoglobulins and T-cell receptors. Here we describe a series of high-resolution X-ray structures that mimic the pre-catalytic state, the post-catalytic state and a competent state that can be transformed into the two other ones in crystallo via the addition of dAMPcPP and Zn(2+), respectively. We examined the effect of Mn(2+), Co(2+) and Zn(2+) because they all have a marked influence on the kinetics of the reaction. We demonstrate a dynamic role of divalent transition metal ions bound to site A: (i) Zn(2+) (or Co(2+)) in Metal A site changes coordination from octahedral to tetrahedral after the chemical step, which explains the known higher affinity of Tdt for the primer strand when these ions are present, and (ii) metal A has to leave to allow the translocation of the primer strand and to clear the active site, a typical feature for a ratchet-like mechanism. Except for Zn(2+), the sugar puckering of the primer strand 3' terminus changes from C2'-endo to C3'-endo during catalysis. In addition, our data are compatible with a scheme where metal A is the last component that binds to the active site to complete its productive assembly, as already inferred in human pol beta. The new structures have potential implications for modeling pol mu, a closely related polX implicated in the repair of DNA double-strand breaks, in a complex with a DNA synapsis.