4W9M | pdb_00004w9m

AMPPNP bound Rad50 in complex with dsDNA

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)
K	SMC_N_1	e4w9mK1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SMC_N_1	ECOD (1.6)
I	SMC_N_1	e4w9mI1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SMC_N_1	ECOD (1.6)
E	SMC_N_1	e4w9mE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SMC_N_1	ECOD (1.6)
C	SMC_N_1	e4w9mC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SMC_N_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
K	1.10.287.660	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
I	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, F, J, L	PF22161	Mre11 C-terminal domain, bacteria (Mre11_C_bact)	Mre11 C-terminal domain, bacteria	This entry represents the helix-turn-helix domain of Mre11 from Thermotoga maritima and similar proteins [1]. It binds Rad50 and attaches flexibly to the nuclease domain which allows large conformational changes.	Domain
C, E, I, K	PF13558	SbcC/RAD50-like, Walker B motif (SbcC_Walker_B)	SbcC/RAD50-like, Walker B motif	This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is sepa ...	This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is separated of the Walker A domain by a long coiled-coil domain and forms the nucleotide-binding domain (NBD) when the coiled coils fold back on themselves and bring together Walker A and B domains [1,2,3,4]. Two RAD50-NBDs forms heterotetramers with a Mre11 nuclease dimer that assemble as catalytic head module that binds and cleaves DNA in an ATP-dependent reaction. Through secondary structural analysis, it has been suggested that there is a wide structural conservation in the Rad50/SMC protein family as seen in structural similarities between RAD50's hook and ABC-ATPase MukB's elbow region [4].	Domain
C, E, I, K	PF13476	AAA domain (AAA_23)	AAA domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F, J, L	Exonuclease, putative	DNA binding binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA exonuclease activity catalytic activity, acting on DNA DNA nuclease activity DNA endonuclease activity DNA binding binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA exonuclease activity catalytic activity, acting on DNA DNA nuclease activity DNA endonuclease activity endonuclease activity cation binding ion binding metal ion binding small molecule 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 response to stimulus cellular response to stress DNA damage response response to stress DNA repair 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 response to stimulus cellular response to stress DNA damage response response to stress DNA repair double-strand break repair DNA recombination	-
C, E, I, K	Probable DNA double-strand break repair Rad50 ATPase,Probable DNA double-strand break repair Rad50 ATPase	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 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 hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity DNA exonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid exonuclease activity DNA nuclease activity cation binding metal ion binding	cellular response to stimulus double-strand break repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	protein-containing complex catalytic complex DNA repair complex
B [auth A], H [auth G]	DNA (5'-D(GPGPTPCPGPGPTPCPAPCPCPGPAPCP*C)-3')	-	-	-
A [auth Y], G [auth Z]	DNA (5'-D(GPGPTPCPGPGPTPGPAPCPCPGPAPCP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, F, J, L	IPR054045	Mre11, C-terminal domain	Domain
D, F, J, L	IPR054406	Mre11, accessory DNA binding capping domain	Domain
D, F, J, L	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
D, F, J, L	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
D, F, J, L	IPR004593	Nuclease SbcCD subunit D	Family
D, F, J, L	IPR050535	DNA Repair and Maintenance Complex Component	Family
D, F, J, L	IPR041796	DNA double-strand break repair protein Mre11, N-terminal metallophosphatase domain	Domain
C, E, I, K	IPR013134	RAD50, zinc hook	Domain
C, E, I, K	IPR038729	Rad50/SbcC-type AAA domain	Domain
C, E, I, K	IPR029012	Helix hairpin bin domain superfamily	Homologous Superfamily
C, E, I, K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.