2RDJ | pdb_00002rdj

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth B]	d2rdjb1	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	DinB homolog (DBH)	( ) [TaxId: ], (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) ) [TaxId: 273057 ],	SCOPe (2.08)
F [auth B]	d2rdjb2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DinB homolog (DBH)	( ) [TaxId: ], (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) ) [TaxId: 273057 ],	SCOPe (2.08)
E [auth A]	d2rdja1	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	DinB homolog (DBH)	( ) [TaxId: ], (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) ) [TaxId: 273057 ],	SCOPe (2.08)
E [auth A]	d2rdja2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DinB homolog (DBH)	( ) [TaxId: ], (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) ) [TaxId: 273057 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Ta1206-like	8055757	3001431	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	3000579	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	3000579	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Ta1206-like	8055757	3001431	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)
F [auth B]		e2rdjB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH_1	F:	ECOD (20:10:01)
F [auth B]		e2rdjB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
F [auth B]		e2rdjB3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
F [auth B]		e2rdjB4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)
E [auth A]		e2rdjA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: IMS_HHH	F:	ECOD (20:10:01)
E [auth A]		e2rdjA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
E [auth A]		e2rdjA3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
E [auth A]		e2rdjA4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Pkinase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth B]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
F [auth B]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
F [auth B]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F [auth B]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
E [auth A]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
E [auth A]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
E [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
E [auth A]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
E [auth A], F [auth B]	PF11799	impB/mucB/samB family C-terminal domain (IMS_C)	impB/mucB/samB family C-terminal domain	These proteins are involved in UV protection (Swiss).	Domain
E [auth A], F [auth B]	PF11798	IMS family HHH motif (IMS_HHH)	IMS family HHH motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B]	DNA polymerase IV	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding damaged DNA binding nucleic acid binding	translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress DNA damage response response to stress metabolic process cellular process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA repair DNA-templated DNA replication	cellular anatomical structure intracellular anatomical structure cytoplasm
D [auth F]	DNA (5'-D(PDTPDAPDTPDTPDCPDGPDAPDAPDGPDGPDGPDTPDCPDCP*DC)-3')	-	-	-
B [auth D]	DNA (5'-D(PDTPDTPDAPDTPDTPDCPDGPDAPDAPDGPDGPDGPDTPDCPDCPDC)-3')	-	-	-
A [auth C], C [auth E]	DNA (5'-D(DGPDGPDGPDAPDCPDCPDCPDTPDTPDCPDGPDAPDAPDT)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR001126	UmuC domain	Domain
E [auth A], F [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
E [auth A], F [auth B]	IPR050116	DNA polymerase type-Y	Family
E [auth A], F [auth B]	IPR022880	DNA polymerase IV	Family
E [auth A], F [auth B]	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
E [auth A], F [auth B]	IPR024728	DNA polymerase type-Y, HhH motif	Conserved Site

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.