8UK9

Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog

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)
A	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8092970	3000691	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Post-AAA+ oligomerization domain-like	8092970	3000691	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA clamp	8036423	3000780	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA clamp	8036422	3000780	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, Q	PF16790	Bacteriophage clamp loader A subunit (Phage_clamp_A)	Bacteriophage clamp loader A subunit	This is the A subunit of bacteriophage DNA clamp loader required for loading of sliding clamps onto chromosomal DNA. These clamps are involved in processivity of DNA replication [1].	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	PF21328	Sliding-clamp-loader large subunit, AAA+ ATPase lid domain (Gp44_lid)	Sliding-clamp-loader large subunit, AAA+ ATPase lid domain	Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA+ superfamily of ATPases which form pentameric complexes that load sliding DNA c ...	Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA+ superfamily of ATPases which form pentameric complexes that load sliding DNA clamps onto the DNA, key for processive chromosomal replication [1,2]. This entry represents the AAA+ ATPase lid domain.	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	PF21429	Sliding-clamp-loader large subunit, C-terminal domain (Gp44_C)	Sliding-clamp-loader large subunit, C-terminal domain	This domain is found at the C-terminal end of Sliding-clamp-loader large subunit from Bacteriophage T4 (Gp44) and similar proteins predominantly found in tailed bacteriophages. Gp44 functions as an ATPase enzyme. It also contains an AAA module (Pfam: ...	This domain is found at the C-terminal end of Sliding-clamp-loader large subunit from Bacteriophage T4 (Gp44) and similar proteins predominantly found in tailed bacteriophages. Gp44 functions as an ATPase enzyme. It also contains an AAA module (Pfam:PF00004) [1,2].	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain
F, G, H, R, S F, G, H, R, S, T	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
F, G, H, R, S F, G, H, R, S, T	PF02916	DNA polymerase processivity factor (DNA_PPF)	DNA polymerase processivity factor	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, Q	Sliding-clamp-loader small subunit	DNA binding binding organic cyclic compound binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity	nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication cellular process DNA biosynthetic process	-
B, C, D, E, K B, C, D, E, K, L, M, N	Sliding-clamp-loader large subunit	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA clamp loader activity catalytic activity ATP-dependent activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	cellular biosynthetic process cellular 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 cellular biosynthetic process cellular 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 cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA-templated DNA replication DNA replication	intracellular organelle protein-containing complex intracellular anatomical structure DNA replication factor C complex organelle intracellular non-membrane-bounded organelle replication fork chromosome cellular anatomical entity non-membrane-bounded organelle
F, G, H, R, S F, G, H, R, S, T	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 primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral gene expression viral process viral transcription cellular biosynthetic process cellular metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral gene expression viral process viral transcription cellular biosynthetic process cellular metabolic process 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 cellular process DNA biosynthetic process	-
I, O	DNA template	-	-	-
J, P	DNA primer	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, Q	IPR031868	Sliding-clamp-loader small subunit gp62	Family
B, C, D, E, K B, C, D, E, K, L, M, N	IPR050238	DNA Replication and Repair Clamp Loader Complex	Family
B, C, D, E, K B, C, D, E, K, L, M, N	IPR046388	Sliding-clamp-loader large subunit	Family
B, C, D, E, K B, C, D, E, K, L, M, N	IPR048815	Sliding-clamp-loader large subunit, AAA+ ATPase lid domain	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	IPR048817	Sliding-clamp-loader large subunit, C-terminal domain	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	IPR003593	AAA+ ATPase domain	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	IPR003959	ATPase, AAA-type, core	Domain
B, C, D, E, K B, C, D, E, K, L, M, N	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
F, G, H, R, S F, G, H, R, S, T	IPR046938	DNA clamp superfamily	Homologous Superfamily
F, G, H, R, S F, G, H, R, S, T	IPR046389	Sliding clamp	Family
F, G, H, R, S F, G, H, R, S, T	IPR004190	DNA polymerase processivity factor	Domain
F, G, H, R, S F, G, H, R, S, T	IPR015200	Sliding clamp, C-terminal	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 R01GM157729.