1JMS

Crystal Structure of the Catalytic Core of Murine Terminal Deoxynucleotidyl Transferase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jmsa1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase beta, N-terminal domain-like	Terminal deoxynucleotidyl transferase	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1jmsa3	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	Terminal deoxynucleotidyl transferase	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1jmsa4	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	Terminal deoxynucleotidyl transferase	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DNA polymerase beta-like	8029744	4001836	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA polymerase beta N-terminal domain-like	8024786	4001032	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA polymerase beta-like second domain	8029743	4002153	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidyltransferase-like	8042123	3000129	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA polymerase beta N-terminal domain-like	8037165	3000524	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PsbU/PolX domain-like	8042122	3000893	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_pol_lambd_f	e1jmsA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
A	HHH_8	e1jmsA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
A	DNA_pol_B_palm	e1jmsA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14716	Helix-hairpin-helix domain (HHH_8)	Helix-hairpin-helix domain	-	Domain
A	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
A	PF10391	Fingers domain of DNA polymerase lambda (DNA_pol_lambd_f)	Fingers domain of DNA polymerase lambda	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 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
A	PF01909	Nucleotidyltransferase domain (NTP_transf_2)	Nucleotidyltransferase domain	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. 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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE	hydrolase activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA nucleotidylexotransferase activity hydrolase activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA nucleotidylexotransferase activity cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process macromolecule modification metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process response to organic substance response to stimulus response to chemical response to organonitrogen compound nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA modification organic substance metabolic process macromolecule modification metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process response to organic substance response to stimulus response to chemical response to organonitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to ATP response to purine-containing compound response to organic cyclic compound cellular response to stimulus double-strand break repair double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress cellular process DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix cytoplasm membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle nuclear periphery nuclear lumen nuclear matrix cytoplasm cytosol nucleoplasm protein-containing complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle euchromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
A	IPR019843	DNA polymerase family X, binding site	Binding Site
A	IPR001726	DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu	Family
A	IPR029398	DNA polymerase beta, thumb domain	Domain
A	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A	IPR001357	BRCT domain	Domain
A	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
A	IPR036420	BRCT domain superfamily	Homologous Superfamily
A	IPR027292	DNA nucleotidylexotransferase (TdT)	Family
A	IPR022312	DNA polymerase family X	Family
A	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
A	IPR018944	DNA polymerase lambda, fingers domain	Domain
A	IPR002934	Polymerase, nucleotidyl transferase domain	Domain
A	IPR002054	DNA-directed DNA polymerase X	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	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] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.7.31 (PDB Primary Data) Search M-CSA Motif + EC 2.7.7.31

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.