1AVQ

TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1avqb_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
A	d1avqa_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
C	d1avqc_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Restriction endonuclease-like	8044442	3000104	SCOP2B (2022-06-29)
A	SCOP2 Family	lambda exonuclease-like	8032064	4000490	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Restriction endonuclease-like	8044442	3000104	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Restriction endonuclease-like	8044442	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)
B	YqaJ	e1avqB1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YqaJ	ECOD (1.6)
A	YqaJ	e1avqA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YqaJ	ECOD (1.6)
C	YqaJ	e1avqC1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: YqaJ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)
A	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)
C	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09588	YqaJ-like viral recombinase domain (YqaJ)	YqaJ-like viral recombinase domain	This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a ...	This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	LAMBDA EXONUCLEASE	DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid double-stranded DNA 5'-3' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity DNA exonuclease activity 5'-3' exonuclease activity catalytic activity, acting on a nucleic acid double-stranded DNA 5'-3' DNA exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity 5'-3' DNA exonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR019080	YqaJ viral recombinase	Domain
A, B, C	IPR011604	PD-(D/E)XK endonuclease-like domain superfamily	Homologous Superfamily
A, B, C	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B, C	IPR051703	NF-kappa-B Signaling Regulator	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	exodeoxyribonuclease (lambda-induced) M-CSA #836	Lambda-exonuclease from Bacteriophage lambda is a 5'->3' exonuclease. It catalyses the hydrolysis of one strand of double stranded DNA in a 5' to 3' direction, leaving single stranded DNA. This is involved in DNA replication, recombination and repair. Once started on a reaction, lambda-exonuclease will continue to hydrolyse until either the DNA strand ends, or the enzyme dissociates into monomers.	Defined by 6 residues: GLU:A-95 [auth A-93]GLU:A-104 [auth A-102]ASP:A-111 [auth A-109]GLU:A-131 [auth A-129]LEU:A-132 [auth A-130]LYS:A-133 [auth A-131] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.11.3 (PDB Primary Data) Search M-CSA Motif + EC 3.1.11.3

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.