Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2 FamilyDNA polymerase beta, N-terminal domain-like 8024786 4001032 SCOP2 (2022-06-29)
ASCOP2 FamilyDNA polymerase beta-like, second domain 8029743 4002153 SCOP2 (2022-06-29)
ASCOP2 FamilyDNA polymerase beta-like 8029744 4001836 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyDNA polymerase beta, N-terminal domain-like 8037165 3000524 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyPsbU/PolX domain-like 8042122 3000893 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyNucleotidyltransferase-like 8042123 3000129 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ADNA_pol_lambd_fe1jmsA1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: DNA_pol_lambd_fECOD (1.6)
AHHH_8e1jmsA2 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: HHH_8ECOD (1.6)
ADNA_pol_B_palme1jmsA3 A: a+b three layersX: Nucleotidyltransferase-likeH: Nucleotidyltransferase (From Topology)T: NucleotidyltransferaseF: DNA_pol_B_palmECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A1.10.150.110 Mainly Alpha Orthogonal Bundle DNA polymerase domain 1CATH (4.3.0)
A1.10.150.20 Mainly Alpha Orthogonal Bundle DNA polymerase domain 1CATH (4.3.0)
A3.30.460.10 Alpha Beta 2-Layer Sandwich Beta Polymerase domain 2CATH (4.3.0)
A3.30.210.10 Alpha Beta 2-Layer Sandwich Beta Polymerase domain 3CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF14716Helix-hairpin-helix domain (HHH_8)Helix-hairpin-helix domain- Domain
PF14791DNA polymerase beta thumb (DNA_pol_B_thumb)DNA polymerase beta thumb- Family
PF10391Fingers domain of DNA polymerase lambda (DNA_pol_lambd_f)Fingers domain of DNA polymerase lambdaDNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the centr ...DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone [1].
Domain
PF01909Nucleotidyltransferase domain (NTP_transf_2)Nucleotidyltransferase domainMembers of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTa ...Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
DNA nucleotidylexotransferase  M-CSA #632

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 and lambda, 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. Tdt is unique in this respect due to its ability to be catalytically active with a range of divalent cations bound, Co2+, Mn2+, Zn2+and Mg2+. The ion bound determines substrate specificity and the enzyme's kinetics.

Defined by 3 residues: ASP:A-214 [auth A-343]ASP:A-216 [auth A-345]ASP:A-305 [auth A-434]
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