1TAE

Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal

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	d1taea_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	Adenylation domain of NAD+-dependent DNA ligase	Adenylation domain of NAD+-dependent DNA ligase	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
B	d1taeb_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	Adenylation domain of NAD+-dependent DNA ligase	Adenylation domain of NAD+-dependent DNA ligase	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
C	d1taec_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	Adenylation domain of NAD+-dependent DNA ligase	Adenylation domain of NAD+-dependent DNA ligase	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)
D	d1taed_	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	Adenylation domain of NAD+-dependent DNA ligase	Adenylation domain of NAD+-dependent DNA ligase	(Enterococcus faecalis V583 ) [TaxId: 226185 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8042451	3000798	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8042451	3000798	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8042451	3000798	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8042451	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)
A	DNA_ligase_aden	e1taeA2	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)
B	DNA_ligase_aden	e1taeB2	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)
C	DNA_ligase_aden	e1taeC2	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)
D	DNA_ligase_aden	e1taeD2	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)
A	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
B	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
C	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D	1.10.287.610	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
D	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)

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, NAD-dependent	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 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 nucleobase-containing compound metabolic process DNA replication metabolic 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 cellular process DNA repair	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

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 R01GM133198.