Annotations: 3UPU

Crystal structure of the T4 Phage SF1B Helicase Dda

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	AAA_19	e3upuC4	A: beta barrels	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: AAA_19	ECOD (v294.2)
C	Vps4_C,AAA_lid_3	e3upuC6	A: beta barrels	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: Vps4_C,AAA_lid_3	ECOD (v294.2)
B		e3upuB4	A: beta barrels	X: PH domain-like	H: PH domain-like	T: PH domain-like	F:	ECOD (v294.2)
A	A2M_BRD	e3upuA1	A: beta barrels	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: A2M_BRD	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	2.30.30.780	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.30.30.780	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.30.30.780	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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
A, B, C	PF13538	UvrD-like helicase C-terminal domain (UvrD_C_2)	UvrD-like helicase C-terminal domain	This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.	Domain
A, B, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	5'-D(TPTPTPTPTPTPTPT)-3'	-	-	-
A, B, C	ATP-dependent DNA helicase dda	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity binding adenyl ribonucleotide binding nucleotide binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity 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	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR051055	PIF1 DNA helicase	Family
A, B, C	IPR041214	Dda helicase SH3 domain	Domain
A, B, C	IPR003593	AAA+ ATPase domain	Domain
A, B, C	IPR027785	UvrD-like helicase C-terminal domain	Domain
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.