1RZT

Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
M [auth A]	d1rzta1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M [auth A]	d1rzta2	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M [auth A]	d1rzta3	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N [auth E]	d1rzte1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N [auth E]	d1rzte2	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N [auth E]	d1rzte3	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
O [auth I]	d1rzti1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
O [auth I]	d1rzti2	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
O [auth I]	d1rzti3	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
P [auth M]	d1rztm1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase beta, N-terminal domain-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
P [auth M]	d1rztm2	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
P [auth M]	d1rztm3	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase lambda	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
M [auth A]	SCOP2B Superfamily	DNA polymerase beta, N-terminal domain-like	8037849	3000524	SCOP2B (2022-06-29)
M [auth A]	SCOP2B Superfamily	PsbU/PolX domain-like	8037850	3000893	SCOP2B (2022-06-29)
M [auth A]	SCOP2B Superfamily	Nucleotidyltransferase-like	8037852	3000129	SCOP2B (2022-06-29)
N [auth E]	SCOP2B Superfamily	PsbU/PolX domain-like	8037850	3000893	SCOP2B (2022-06-29)
N [auth E]	SCOP2B Superfamily	DNA polymerase beta, N-terminal domain-like	8037849	3000524	SCOP2B (2022-06-29)
N [auth E]	SCOP2B Superfamily	Nucleotidyltransferase-like	8037852	3000129	SCOP2B (2022-06-29)
O [auth I]	SCOP2B Superfamily	Nucleotidyltransferase-like	8037852	3000129	SCOP2B (2022-06-29)
O [auth I]	SCOP2B Superfamily	DNA polymerase beta, N-terminal domain-like	8037849	3000524	SCOP2B (2022-06-29)
O [auth I]	SCOP2B Superfamily	PsbU/PolX domain-like	8037850	3000893	SCOP2B (2022-06-29)
P [auth M]	SCOP2B Superfamily	Nucleotidyltransferase-like	8037852	3000129	SCOP2B (2022-06-29)
P [auth M]	SCOP2B Superfamily	PsbU/PolX domain-like	8037850	3000893	SCOP2B (2022-06-29)
P [auth M]	SCOP2B Superfamily	DNA polymerase beta, N-terminal domain-like	8037849	3000524	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
M [auth A]	DNA_pol_lambd_f	e1rztA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
M [auth A]	HHH_8	e1rztA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
M [auth A]	DNA_pol_B_palm	e1rztA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
N [auth E]	DNA_pol_lambd_f	e1rztE1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
N [auth E]	HHH_8	e1rztE2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
N [auth E]	DNA_pol_B_palm	e1rztE3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
O [auth I]	DNA_pol_lambd_f	e1rztI1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
O [auth I]	HHH_8	e1rztI2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
O [auth I]	DNA_pol_B_palm	e1rztI3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
P [auth M]	DNA_pol_lambd_f	e1rztM1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
P [auth M]	HHH_8	e1rztM2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
P [auth M]	DNA_pol_B_palm	e1rztM3	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)
M [auth A]	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
M [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
M [auth A]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
M [auth A]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
N [auth E]	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
N [auth E]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
N [auth E]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
N [auth E]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
O [auth I]	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
O [auth I]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
O [auth I]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
O [auth I]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
P [auth M]	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
P [auth M]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
P [auth M]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
P [auth M]	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
M [auth A], N [auth E], O [auth I], P [auth M]	PF14716	Helix-hairpin-helix domain (HHH_8)	Helix-hairpin-helix domain	-	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
M [auth A], N [auth E], O [auth I], P [auth M]	PF14792	DNA polymerase beta palm (DNA_pol_B_palm)	DNA polymerase beta palm	The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain [1].	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], F [auth H], I [auth L], L [auth P]	5'-D(PGPCPCPG)-3'	-	-	-
A [auth B], D [auth F], G [auth J], J [auth N]	5'-D(CPGPGPCPAPAPCPGPCPAP*C)-3'	-	-	-
B [auth C], E [auth G], H [auth K], K [auth O]	5'-D(GPTPGPCP*G)-3'	-	-	-
M [auth A], N [auth E], O [auth I], P [auth M]	DNA polymerase lambda	catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process immune system development developmental process production of molecular mediator of immune response multicellular organismal process immunoglobulin production cellular biosynthetic process somatic diversification of immune receptors via somatic mutation nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process immune system development developmental process production of molecular mediator of immune response multicellular organismal process immunoglobulin production cellular biosynthetic process somatic diversification of immune receptors via somatic mutation cellular metabolic process gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins multicellular organism development biosynthetic process immune system process anatomical structure development somatic diversification of immune receptors cellular process somatic hypermutation of immunoglobulin genes system development nucleobase-containing compound biosynthetic process nucleic acid biosynthetic process DNA biosynthetic process cellular response to stimulus double-strand break repair response to stimulus DNA recombination cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair nucleotide-excision repair base-excision repair, gap-filling base-excision repair double-strand break repair via nonhomologous end joining	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M [auth A], N [auth E], O [auth I], P [auth M]	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
M [auth A], N [auth E], O [auth I], P [auth M]	IPR019843	DNA polymerase family X, binding site	Binding Site
M [auth A], N [auth E], O [auth I], P [auth M]	IPR029398	DNA polymerase beta, thumb domain	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	IPR002008	DNA polymerase family X, beta-like	Family
M [auth A], N [auth E], O [auth I], P [auth M]	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
M [auth A], N [auth E], O [auth I], P [auth M]	IPR001357	BRCT domain	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
M [auth A], N [auth E], O [auth I], P [auth M]	IPR036420	BRCT domain superfamily	Homologous Superfamily
M [auth A], N [auth E], O [auth I], P [auth M]	IPR028207	DNA polymerase beta, palm domain	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	IPR022312	DNA polymerase family X	Family
M [auth A], N [auth E], O [auth I], P [auth M]	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	IPR018944	DNA polymerase lambda, fingers domain	Domain
M [auth A], N [auth E], O [auth I], P [auth M]	IPR002054	DNA-directed DNA polymerase X	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
M [auth A], N [auth E], O [auth I], P [auth M]	Pharos: Q9UGP5	osteosarcoma xeroderma pigmentosum

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.