1KDH

Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA

Summary for 1KDH

• Entry DOI: 10.2210/pdb1kdh/pdb
• Related: 1BPY 1JMS 1KEJ
• Descriptor: 5'-D(P*(BRU)P*(BRU)P*(BRU)P*(BRU))-3', Terminal deoxynucleotidyltransferase short isoform, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: polymerase, nucleotidyl transferase, transferase-dna complex, transferase/dna
• Biological source: Mus musculus (house mouse)
• Total number of polymer chains: 2
• Total formula weight: 43394.43

Authors

Delarue, M.,Boule, J.B.,Lescar, J.,Expert-Bezancon, N.,Jourdan, N.,Sukumar, N.,Rougeon, F.,Papanicolaou, C. (deposition date: 2001-11-13, release date: 2002-05-13, Last modification date: 2023-08-16)

Primary citation

Delarue, M.,Boule, J.B.,Lescar, J.,Expert-Bezancon, N.,Jourdan, N.,Sukumar, N.,Rougeon, F.,Papanicolaou, C.
Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
EMBO J., 21:427-439, 2002

PubMed Abstract: The crystal structure of the catalytic core of murine terminal deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA polymerase beta-like fold locked in a closed form. In addition, the structures of two different binary complexes, one with an oligonucleotide primer and the other with an incoming ddATP-Co(2+) complex, show that the substrates and the two divalent ions in the catalytic site are positioned in TdT in a manner similar to that described for the human DNA polymerase beta ternary complex, suggesting a common two metal ions mechanism of nucleotidyl transfer in these two proteins. The inability of TdT to accommodate a template strand can be explained by steric hindrance at the catalytic site caused by a long lariat-like loop, which is absent in DNA polymerase beta. However, displacement of this discriminating loop would be sufficient to unmask a number of evolutionarily conserved residues, which could then interact with a template DNA strand. The present structure can be used to model the recently discovered human polymerase mu, with which it shares 43% sequence identity.

PubMed: 11823435
DOI: 10.1093/emboj/21.3.427

Experimental method

X-RAY DIFFRACTION (3 Å)