3SM4

Crystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3sm4a_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
B	d3sm4b1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
B	d3sm4b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
C	d3sm4c1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	lambda exonuclease	lambda exonuclease	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
C	d3sm4c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A	SCOP2B Superfamily	Restriction endonuclease-like	8044442	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8044442	3000104	SCOP2B (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)
A	YqaJ	e3sm4A1	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)
B	YqaJ	e3sm4B1	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	e3sm4C1	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)
A	3.90.320.10	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)
B	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	Exonuclease	nuclease activity hydrolase activity, acting on ester bonds hydrolase activity exonuclease activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-
D	5'-D(TPCPGPGPTPAPCPAPGPTPAPG)-3'	-	-	-
E	5'-D(PAPGPCPTPAPCPTPGPTPAPCPCPGPA)-3'	-	-	-

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.