2OWO

Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate

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)
D [auth A]	DNA_ligase_OB	e2owoA3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_OB	ECOD (1.6)
D [auth A]	HHH_2	e2owoA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_2	ECOD (1.6)
D [auth A]	DNA_ligase_aden	e2owoA4	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: DNA_ligase_aden	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
D [auth A]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D [auth A]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D [auth A]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D [auth A]	6.20.10.30	Special	Other non-globular	Laminin		CATH (4.3.0)
D [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A]	PF00633	Helix-hairpin-helix motif (HHH)	Helix-hairpin-helix motif	-	Motif
D [auth A]	PF03119	NAD-dependent DNA ligase C4 zinc finger domain (DNA_ligase_ZBD)	NAD-dependent DNA ligase C4 zinc finger domain	DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small zinc binding motif that is presumably DNA binding [1] ...	DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small zinc binding motif that is presumably DNA binding [1]. IT is found only in NAD dependent DNA ligases [1].	Domain
D [auth A]	PF03120	NAD-dependent DNA ligase OB-fold domain (DNA_ligase_OB)	NAD-dependent DNA ligase OB-fold domain	DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small domain found after the adenylation domain Pfam:PF0165 ...	DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This family is a small domain found after the adenylation domain Pfam:PF01653 in NAD dependent ligases [1]. OB-fold domains generally are involved in nucleic acid binding.	Domain
D [auth A]	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain	-	Domain
D [auth A]	PF01653	NAD-dependent DNA ligase adenylation domain (DNA_ligase_aden)	NAD-dependent DNA ligase adenylation domain	DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This domain is the catalytic adenylation domain. The NAD+ group is covalent ...	DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor [1]. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism [1].	Domain
D [auth A]	PF22745	DNA ligase-like, N-terminal NAD+-binding domain (Nlig-Ia)	DNA ligase-like, N-terminal NAD+-binding domain	The alpha-helical Nlig-Ia domain is found at the N-terminal of DNA ligases and it has been proposed to either swivel the NAD+ close to the ligase active site lysine on the RAGNYA domain or function as an allosteric NAD+ binding site. The Nlig-Ia doma ...	The alpha-helical Nlig-Ia domain is found at the N-terminal of DNA ligases and it has been proposed to either swivel the NAD+ close to the ligase active site lysine on the RAGNYA domain or function as an allosteric NAD+ binding site. The Nlig-Ia domain is also observed as a solo protein in phages that do not encode a separate NAD+-dependent ligase catalytic module, suggesting the domain can function independently of a DNA ligase. It has been proposed that these domains likely function as NAD+ sensors which might help indicate to the phage the development of NADase host effectors or shield NAD+ from the action of such effectors [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	26-MER	-	-	-
B [auth C]	5'-D(APCPAPAPTPTPGPCPGPAPCP(OMC)P*C)-3'	-	-	-
C [auth D]	5'-D(CPAPCPTPAPTPCPGPGPAPAPTP*G)-3'	-	-	-
D [auth A]	DNA ligase	ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase (NAD+) activity DNA ligase activity ligase activity DNA binding binding organic cyclic compound binding nucleic acid binding NAD+ binding NAD binding nucleotide binding ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase (NAD+) activity DNA ligase activity ligase activity DNA binding binding organic cyclic compound binding nucleic acid binding NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding 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 response to stimulus base-excision repair, DNA ligation DNA ligation involved in DNA repair DNA ligation base-excision 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 base-excision repair, DNA ligation DNA ligation involved in DNA repair DNA ligation base-excision repair cellular response to stress DNA damage response response to stress DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A]	IPR041663	DisA/LigA, helix-hairpin-helix motif	Domain
D [auth A]	IPR004149	Zinc-finger, NAD-dependent DNA ligase C4-type	Domain
D [auth A]	IPR001679	NAD-dependent DNA ligase	Family
D [auth A]	IPR010994	RuvA domain 2-like	Homologous Superfamily
D [auth A]	IPR001357	BRCT domain	Domain
D [auth A]	IPR018239	NAD-dependent DNA ligase, active site	Active Site
D [auth A]	IPR013840	NAD-dependent DNA ligase, N-terminal	Domain
D [auth A]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
D [auth A]	IPR013839	NAD-dependent DNA ligase, adenylation	Domain
D [auth A]	IPR004150	NAD-dependent DNA ligase, OB-fold	Domain
D [auth A]	IPR033136	NAD-dependent DNA ligase, conserved site	Conserved Site
D [auth A]	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
D [auth A]	IPR036420	BRCT domain superfamily	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.