6HMS

Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8053389	3001067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8053391	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8055689	3001330	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)
B	PF03833	e6hmsB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: PF03833	ECOD (1.6)
B	PF03833	e6hmsB3	A: beta barrels	X: cradle loop barrel	H: DP2 DPBB-1 domain (From Topology)	T: DP2 DPBB-1 domain	F: PF03833	ECOD (1.6)
B	PF03833	e6hmsB5	A: alpha arrays	X: HTH	H: DNA polymerase II large subunit DP2 helical domain (From Topology)	T: DNA polymerase II large subunit DP2 helical domain	F: PF03833	ECOD (1.6)
B	PF03833	e6hmsB4	A: a+b two layers	X: Homing endonucleases-like	H: DNA polymerase II large subunit DP2 central a+b domain (From Topology)	T: DNA polymerase II large subunit DP2 central a+b domain	F: PF03833	ECOD (1.6)
B	PF03833	e6hmsB1	A: a+b two layers	X: DNA polymerase D large subunit DP2 N-terminal domain (From Topology)	H: DNA polymerase D large subunit DP2 N-terminal domain (From Topology)	T: DNA polymerase D large subunit DP2 N-terminal domain	F: PF03833	ECOD (1.6)
B	F_UNCLASSIFIED	e6hmsB7	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF03833	e6hmsB6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF03833	ECOD (1.6)
B	F_UNCLASSIFIED	e6hmsB8	A: few secondary structure elements	X: Rubredoxin-like	H: Zinc finger domain of DNA polymerase-alpha (From Topology)	T: Zinc finger domain of DNA polymerase-alpha	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain
B	PF03833	DNA polymerase II large subunit DP2 (PolC_DP2)	DNA polymerase II large subunit DP2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase II small subunit	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 DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease 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 catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process DNA-templated DNA replication DNA replication	-
B	DNA polymerase II large subunit,DNA polymerase II large subunit	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 DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease 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 catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process intein-mediated protein splicing organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis organic substance biosynthetic process protein processing cellular process protein metabolic process protein splicing DNA-templated DNA replication DNA replication	-
C [auth P]	DNA (5'-D(GPAPGPAPCPGPGPGPCPCPGPCPGPTP*C)-3')	-	-	-
D [auth T]	DNA (5'-D(PTPGPAPCPGPCPGPGPCPCPCPGPTPCPTPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR011149	DNA polymerase II small subunit, archaeal	Family
A	IPR024826	DNA polymerase delta/II small subunit family	Family
A	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
B	IPR006141	Intein N-terminal splicing region	PTM
B	IPR016033	DNA polymerase II large subunit DP2, N-terminal	Domain
B	IPR036844	Hint domain superfamily	Homologous Superfamily
B	IPR003587	Hint domain N-terminal	Domain
B	IPR004475	DNA polymerase II large subunit DP2	Family
B	IPR030934	Intein C-terminal splicing region	Domain

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 R01GM133198.