7K72 | pdb_00007k72

Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	d7k72d_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d7k72c_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d7k72b_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d7k72a_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8067856	3000798	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8067856	3000798	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8067856	3000798	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8067856	3000798	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)
D	V-set	e7k72D1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (develop294)
C	V-set	e7k72C1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (develop294)
B	V-set	e7k72B1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (develop294)
A	V-set	e7k72A1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	DNA ligase A	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 magnesium ion 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 cell periphery plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

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