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Catalytic Site Atlas

CSA LITERATURE entry for 1jms

E.C. nameDNA nucleotidylexotransferase
SpeciesMus musculus (Mouse)
E.C. Number (IntEnz)
CSA Homologues of 1jmsThere are 155 Homologs
CSA Entries With UniProtID P09838
CSA Entries With EC Number
PDBe Entry 1jms
PDBSum Entry 1jms
MACiE Entry 1jms

Literature Report

IntroductionTerminal deoxynucleotidyl transferase (TdT) catalyses the condensation of deoxyribonucleotide triphosphates onto the 3' hydroxyl ends of DNA strands in a template-independent manner. It can also catalyse the addition of ribonucleotides and a range of unnatural nucleotides onto DNA strands. TdT has only been found in mammals, where it is highly conserved. It has a role in the generation of combinatorial diversity in lymphocytes, where it functions to add nucleotides (N regions) to the V(D)J recombination junctions of immunoglobulin and T-cell receptor genes. Together with DNA polymerase beta, TdT belongs to a family of polymerases called pol X, a subclass of an ancient nucleotidyl transferase (NT) superfamily. The active site of this family is structurally similar to that of the pol I and pol alpha families even though the topology of the catalytic domain is different; in all cases the active site is made up of three carboxylate side chains which bind two divalent cations.
MechansimBy analogy with DNA polymerase beta, TdT uses an Mg2+ ion to promote attack by the 3' hydroxyl group of the primer on the alpha phosphorous of the incoming NTP. Coordination of the 3' hydroxyl group to the Mg2+ ion lowers the pKa of this group to allow deprotonation by Asp 434 during attack on the NTP. The Mg2+ ion also provides a positive charge to stabilise the pentacoordinate transition state of the alpha phosphorous.

Catalytic Sites for 1jms

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA434434macie:sideChainAccepts proton from attacking 3' OH group of primer.

Literature References

Notes:There are two residues; Asp 343 and Asp 345, which act electrostatically on both Mg2+ ions, keeping them in position. They do not appear to be catalytic, only binding.
Boulé JB
Terminal deoxynucleotidyl transferase indiscriminately incorporates ribonucleotides and deoxyribonucleotides.
J Biol Chem 2001 276 31388-31393
PubMed: 11406636
Delarue M
Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
EMBO J 2002 21 427-439
PubMed: 11823435
Pelletier H
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
Science 1994 264 1891-1903
PubMed: 7516580