6HMS | pdb_00006hms

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)
B	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8055689	3001330	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PolC_DP2_6th	e6hmsB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: PolC_DP2_6th	ECOD (1.6)
B	PolC_DP2_2nd	e6hmsB3	A: beta barrels	X: cradle loop barrel	H: DP2 DPBB-1 domain (From Topology)	T: DP2 DPBB-1 domain	F: PolC_DP2_2nd	ECOD (1.6)
B	PolC_DP2_3rd	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: PolC_DP2_3rd	ECOD (1.6)
B	PolC_DP2_4th	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: PolC_DP2_4th	ECOD (1.6)
B	PolC_DP2_1st	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: PolC_DP2_1st	ECOD (1.6)
B	PolC_DP2_5th	e6hmsB6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PolC_DP2_5th	ECOD (1.6)
B	IBR_1	e6hmsB7	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: IBR_1	ECOD (1.6)
B	Iron_traffic	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: Iron_traffic	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF03833	DNA polymerase II large subunit DP2, N-terminal (PolC_DP2_N)	DNA polymerase II large subunit DP2, N-terminal	This entry represents the N-terminal domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain shows an alpha beta configuration [1].	Domain
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth T]	DNA (5'-D(PTPGPAPCPGPCPGPGPCPCPCPGPTPCPTPC)-3')	-	-	-
C [auth P]	DNA (5'-D(GPAPGPAPCPGPGPGPCPCPGPCPGPTP*C)-3')	-	-	-
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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase 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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity 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 nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process intein-mediated protein splicing gene expression catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process intein-mediated protein splicing gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process protein splicing DNA-templated DNA replication DNA replication	-
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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase 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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity 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 nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR016033	DNA polymerase II large subunit DP2, N-terminal	Domain
B	IPR036844	Hint domain superfamily	Homologous Superfamily
B	IPR030934	Intein C-terminal splicing region	Conserved Site
B	IPR006141	Intein N-terminal splicing region	PTM
B	IPR056171	DNA polymerase II large subunit DP2, central domain	Domain
B	IPR056172	DNA polymerase II large subunit DP2, catalytic domain	Domain
B	IPR003587	Hint domain N-terminal	Domain
B	IPR004475	DNA polymerase II large subunit DP2	Family
A	IPR054750	DNA polymerase II small subunit, N-terminal domain	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	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
A	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily

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.