8AK4 | pdb_00008ak4

Structure of the C-terminally truncated NAD+-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	MaoC_dehydratas	e8ak4A1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: MaoC_dehydratas	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
A	PF03120	NAD-dependent DNA ligase OB-fold domain (OB_DNA_ligase)	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
A	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 cation binding ion binding 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR041663	DisA/LigA, helix-hairpin-helix motif	Domain
A	IPR004149	Zinc-finger, NAD-dependent DNA ligase C4-type	Domain
A	IPR001679	NAD-dependent DNA ligase	Family
A	IPR010994	RuvA domain 2-like	Homologous Superfamily
A	IPR001357	BRCT domain	Domain
A	IPR013840	NAD-dependent DNA ligase, N-terminal	Domain
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR013839	NAD-dependent DNA ligase, adenylation	Domain
A	IPR004150	NAD-dependent DNA ligase, OB-fold	Domain
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.