9EA3 | pdb_00009ea3

T4 bacteriophage replicative holoenzyme containing triple mutations D75R, Q430E, and K432E in the exonuclease-deficient polymerase

External Resource: Annotation

Domain Annotation: SCOP2 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	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C [auth D], D [auth E]	PF09116	gp45 sliding clamp, C terminal (gp45-slide_C)	gp45 sliding clamp, C terminal	Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo tw ...	Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry [1].	Domain
B, C [auth D], D [auth E]	PF02916	DNA polymerase processivity factor (DNA_PPF)	DNA polymerase processivity factor		Domain
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth T]	DNA (38-MER)	-	-	-
E [auth P]	DNA (5'-AGC TAT GAC CAT GAT TAC GAA TTG ddC-3')	-	-	-
B, C [auth D], D [auth E]	Sliding clamp	enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral gene expression viral process viral transcription viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral gene expression viral process viral transcription viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication bidirectional double-stranded viral DNA replication DNA biosynthetic process	-
A	DNA-directed DNA polymerase	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 hydrolase activity, acting on ester bonds nuclease 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 nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity 3'-5' exonuclease activity hydrolase activity exonuclease activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA replication	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C [auth D], D [auth E]	IPR046938	DNA clamp superfamily	Homologous Superfamily
B, C [auth D], D [auth E]	IPR046389	Sliding clamp	Family
B, C [auth D], D [auth E]	IPR004190	DNA polymerase processivity factor	Domain
B, C [auth D], D [auth E]	IPR015200	Sliding clamp, C-terminal	Domain
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR034749	DNA-directed DNA polymerase T4 type	Family
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR050240	DNA polymerase type-B	Family
A	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	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.