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CSA entry for 1jms
Original Entry
Title:
Transferase
Compound:
Terminal deoxynucleotidyltransferase
Mutant:
No
UniProt/Swiss-Prot:
P09838-TDT_MOUSE
EC Class:
2.7.7.31
Other CSA Entries:
Overview of all sites for 1jms
Homologues of 1jms
Entries for UniProt/Swiss-Prot: P09838
Entries for EC: 2.7.7.31
Other Databases:
PDB entry: 1jms
PDBsum entry: 1jms
UniProt/Swiss-Prot: P09838
IntEnz entry: 2.7.7.31
Literature Report:
Introduction:
Terminal 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.
Mechanism:
By 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.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 434 434Sidechain
Acid/baseSubstrate
Accepts proton from attacking 3' OH group of primer.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11406636 Current protein Structural similarity to homologue of known mechanism
PubMed ID 11406636 Current protein Mutagenesis of residue
PubMed ID 11823435 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
MGA 701 0
ElectrostaticSubstrate
ElectrostaticTransition state
Provides a positive charge to stabilises the pentacoordinate transition state of the alpha phosphorous. Activates attacking 3' OH of the primer by promoting its deprotonation by Asp 434.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7516580 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
NAA 702 0
ElectrostaticSubstrate
Stabilises the phosphate groups in the intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 7516580 Current protein Structural similarity to homologue of known mechanism
PubMed ID 7516580 Current protein Residue is positioned appropriately (ligand position known)
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.
References:
1
Terminal deoxynucleotidyl transferase indiscriminately incorporates ribonucleotides and deoxyribonucleotides
J. B. Boule and F. Rougeon and C. Papanicolaou
J Biol Chem 276, (33) 31388-93, (2001)
11406636
2
Crystal structures of a template-independent DNA polymerase: murine terminal deoxyribonucleotidyl transferase
D. M. Boule and J. Lescar and N. Expert-Bezancon and N. Jourdan and N. Sukumar and F. Rougeon and C. Papanicolaou
EMBO J 21 (3) 427-39, (2002)
11823435
3
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
H. Pelletier and M. R. Sawaya and A. Kumar and S. H. Wilson and J. Kraut
Science 264, (5167) 1891-903, (1994).
7516580
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