8GME | pdb_00008gme

Crystal structure of the gp32-Dda-dT17 complex

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)
C [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041966	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8041966	3000135	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D	PF13604	AAA domain (AAA_30)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.	Domain
B [auth C], D	PF18343	Dda helicase SH3 domain (SH3_14)	Dda helicase SH3 domain	This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta- ...	This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA [1].	Domain
A, C [auth B]	PF08804	gp32 DNA binding protein like (gp32)	gp32 DNA binding protein like	gp32 is a single stranded (ss) DNA binding protein in bacteriophage T4 that is essential for DNA replication, recombination and repair. The ssDNA binding cleft of gp32 comprises regions from three structural subdomains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth P], F [auth Q]	dT17	-	-	-
B [auth C], D	Dda helicase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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 catalytic activity ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase 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	-
A, C [auth B]	gp32	cation binding ion binding binding metal ion binding small molecule binding DNA binding single-stranded DNA binding nucleic acid binding	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 DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process 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 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 DNA biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR051055	PIF1 DNA helicase	Family
B [auth C], D	IPR041214	Dda helicase SH3 domain	Domain
B [auth C], D	IPR003593	AAA+ ATPase domain	Domain
B [auth C], D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C [auth B]	IPR044947	Bacteriophage T4, Gp32, single-stranded DNA-binding superfamily	Homologous Superfamily
A, C [auth B]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, C [auth B]	IPR046395	Bacteriophage T4, Gp32, single-stranded DNA-binding	Family
A, C [auth B]	IPR012339	Bacteriophage T4, Gp32, single-stranded DNA-binding domain	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.