5EAW | pdb_00005eaw

Crystal structure of Dna2 nuclease-helicase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	RecA-like P-loop NTPases	8090891	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8090890	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Restriction endonuclease-like	8090888	3000104	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8090887	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Upf1 beta-barrel domain-like	8090889	3002168	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Upf1 beta-barrel domain-like	8090889	3002168	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8090890	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8090887	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8090891	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8090888	3000104	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)
A	KOG1805_2nd	e5eawA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: KOG1805_2nd	ECOD (1.6)
A	Dna2_N	e5eawA4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Dna2_N	ECOD (1.6)
A	KOG1805_1st	e5eawA3	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S binding domain in Dna2 nuclease-helicase (From Topology)	T: 4Fe-4S binding domain in Dna2 nuclease-helicase	F: KOG1805_1st	ECOD (1.6)
A	AAA_12	e5eawA6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_12	ECOD (1.6)
A	AAA_11_1	e5eawA5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
A	Dna2_C	e5eawA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Dna2_C	ECOD (1.6)
B	KOG1805_2nd	e5eawB4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: KOG1805_2nd	ECOD (1.6)
B	Dna2_N	e5eawB6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Dna2_N	ECOD (1.6)
B	KOG1805_1st	e5eawB2	A: alpha arrays	X: 4Fe-4S binding domain in Dna2	H: 4Fe-4S binding domain in Dna2 nuclease-helicase (From Topology)	T: 4Fe-4S binding domain in Dna2 nuclease-helicase	F: KOG1805_1st	ECOD (1.6)
B	AAA_12	e5eawB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_12	ECOD (1.6)
B	AAA_11_1	e5eawB5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
B	Dna2_C	e5eawB3	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Dna2_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.30.270	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B	2.40.30.270	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21123	Dna2 Rift barrel domain (Dna2_Rift)	Dna2 Rift barrel domain	This entry represents a Rift barrel domain found in the Dna2 protein [1]. This domain lies between the nuclease and helicase domains [1]. The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments ...	This entry represents a Rift barrel domain found in the Dna2 protein [1]. This domain lies between the nuclease and helicase domains [1]. The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity.	Domain
A, B	PF08696	DNA replication factor Dna2 (Dna2)	DNA replication factor Dna2	-	Family
A, B	PF13086	AAA domain (AAA_11)	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.	Domain
A, B	PF13087	AAA domain (AAA_12)	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.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA replication ATP-dependent helicase/nuclease DNA2	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 nuclease activity 5'-flap endonuclease activity endonuclease activity 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 nuclease activity 5'-flap endonuclease activity endonuclease activity hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule 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 DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides single-stranded DNA helicase activity cation binding metal ion 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 cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing cellular response to stress DNA damage response nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA double-strand break processing cellular response to stress DNA damage response response to stress DNA repair DNA replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process RNA catabolic process regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation regulation of macromolecule metabolic process positive regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication DNA-templated DNA replication mitochondrial genome maintenance mitochondrial DNA metabolic process cellular component organization organelle organization mitochondrial DNA replication cellular component organization or biogenesis mitochondrion organization telomere organization chromosome organization telomere maintenance regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cell communication negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling lagging strand elongation DNA strand elongation DNA replication, Okazaki fragment processing DNA strand elongation involved in DNA replication base-excision repair mitochondrial DNA repair nuclear DNA replication cell cycle DNA replication mitotic cell cycle telomere maintenance via semi-conservative replication mitotic telomere maintenance via semi-conservative replication mitotic cell cycle process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen mitochondrial protein-containing complex protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen mitochondrial protein-containing complex protein-containing complex mitochondrion catalytic complex transferase complex mitochondrial matrix DNA polymerase complex transferase complex, transferring phosphorus-containing groups gamma DNA polymerase complex cytoplasm intracellular protein-containing complex intracellular membraneless organelle nucleoid membraneless organelle mitochondrial nucleoid chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
A, B	IPR026851	DNA replication ATP-dependent helicase/nuclease Dna2/JHS1, DEXXQ-box helicase domain	Domain
A, B	IPR045055	DNA2/NAM7-like helicase	Family
A, B	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A, B	IPR048459	DNA2, rift barrel domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR014808	DNA replication factor Dna2, N-terminal	Domain
A, B	IPR011604	PD-(D/E)XK endonuclease-like domain superfamily	Homologous Superfamily
A, B	IPR047187	Upf1-like, C-terminal helicase 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.