EC 6.5.1.2 - Dna ligase (NAD(+)).

_EC 6.5.1.2 Dna ligase (NAD(+)).

47 PDB entries

EC 6.-.-.- Ligases. [3,383 PDB entries]

EC 6.5.-.- Forming phosphoric ester bonds. [208 PDB entries]

EC 6.5.1.- Forming phosphoric ester bonds. [208 PDB entries]

EC 6.5.1.2 Dna ligase (NAD(+)). [47 PDB entries]

1b04

Reaction: NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + Amp + beta- nicotinamide D-nucleotide.

NAD(+)
+ (deoxyribonucleotide)n-3'-hydroxyl
+ 5'-phospho- (deoxyribonucleotide)m
=
(deoxyribonucleotide)n+m
+
AMP
+ beta- nicotinamide D-nucleotide

Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Other name(s): Dna joinase. Dna repair enzyme. polydeoxyribonucleotide synthase (NAD(+)). polydeoxyribonucleotide synthase (NAD+). polynucleotide ligase (NAD(+)). polynucleotide ligase (NAD+).

Comments: The enzyme, typically found in bacteria, catalyzes the ligation of Dna strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex Dna. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by NAD(+), forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[DNA].

Links: [IntEnz] [ExPASy] [KEGG]

There are 47 PDB entries in enzyme class E.C.6.5.1.2

PDB code Protein

1b04

Structure of the adenylation domain of an NAD+ dependent ligase

Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: nca 1503. Gene: lig. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Chains: A, B (310 residues) CATH domains: 3.30.470.30 3.30.1490.70 1.10.287.610

1dgs

Crystal structure of NAD+-dependent DNA ligase from t. Filiformis

Source: Thermus filiformis. Organism_taxid: 276

Chains: A, B (581 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30 2.40.50.140 1.10.150.20 1.10.150.20

Bound ligand: Het Group AMP is 95.65% similar to enzyme product AMP

1l7b

Solution nmr structure of brct domain of t. Thermophilus: northeast structural genomics consortium target wr64tt

Source: Thermus thermophilus. Organism_taxid: 274. Gene: dnlj. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Chain: A (92 residues) CATH domain: 3.40.50.10190

1ta8

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

Source: Enterococcus faecalis. Organism_taxid: 226185. Strain: v583. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (313 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

1tae

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

Source: Enterococcus faecalis. Organism_taxid: 226185. Strain: v583. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B, C, D (321 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NAD corresponds to enzyme reactant NAD(+)

1v9p

Crystal structure of NAD+-dependent DNA ligase

Source: Thermus filiformis. Organism_taxid: 276. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B (584 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30 2.40.50.140 1.10.150.20 1.10.150.20

Bound ligand: Het Group AMP is 95.65% similar to enzyme product AMP

1zau

Adenylation domain of NAD+ dependent DNA ligase from m.Tuberculosis

Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: liga, lig. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Chain: A (321 residues) CATH domains: 1.10.287.610 3.30.470.30

Bound ligand: Het Group AMP is 95.65% similar to enzyme product AMP

2owo

Last stop on the road to repair: structure of e.Coli DNA ligase bound to nicked DNA-adenylate

Source: Synthetic: yes. Other_details: chemically synthesized. Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: liga. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Chain: A (586 residues) CATH domains: 1.10.287.610 3.30.470.30 3.30.1490.70 2.40.50.140 6.20.10.30 1.10.150.20 1.10.150.20

Bound ligand: Het Group AMP corresponds to enzyme product AMP

3ba8

Structural basis for the inhibition of bacterial NAD+ dependent DNA ligase

Source: Enterococcus faecalis. Streptococcus faecalis. Organism_taxid: 1351. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (313 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

3ba9

Structural basis for inhbition of NAD-dependent ligase

Source: Enterococcus faecalis. Streptococcus faecalis. Organism_taxid: 1351. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (313 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

3baa

Structural basis for the inhibition of bacterial NAD+ dependent DNA ligase

Source: Enterococcus faecalis. Streptococcus faecalis. Organism_taxid: 1351. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (312 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

3bab

Structural basis for the inhibition of bacterial NAD+ dependent DNA ligase

Source: Enterococcus faecalis. Streptococcus faecalis. Organism_taxid: 1351. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (312 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

3bac

Structural basis for the inhibition of bacterial NAD+ dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Gene: lign, lig. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (255 residues) CATH domain: 3.30.470.30

3jsl

Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from staphylococcus aureus

Source: Staphylococcus aureus. Organism_taxid: 1280. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B (308 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

3jsn

Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from staphylococcus aureus

Source: Staphylococcus aureus. Organism_taxid: 1280. Gene: liga. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (297 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

3pn1

Novel bacterial NAD+-dependent DNA ligase inhibitors with broad spectrum potency and antibacterial efficacy in vivo

Source: Haemophilus influenzae. Organism_taxid: 727. Gene: liga, lig, lign, hi_1100. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (318 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group IVH is 67.86% similar to enzyme product AMP

3sgi

Crystal structure of DNA ligase a brct domain deleted mutant of mycobacterium tuberculosis

Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv. Gene: lig, liga, mt3094, mtv012.28c, rv3014c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Chain: A (408 residues) CATH domains: 1.10.287.610 3.30.470.30 2.40.50.140

Bound ligand: Het Group AMP is 95.65% similar to enzyme product AMP

3uq8

Structure of adenylation domain of haemophilus influenzae DNA ligases bound to NAD+ in adenylated state.

Source: Haemophilus influenzae. Organism_taxid: 71421. Strain: atcc 51907 / dsm 11121 / kw20 / rd. Gene: liga, lig, lign, hi_1100. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (322 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NAD corresponds to enzyme reactant NAD(+)

4cc5

Fragment-based discovery of 6 azaindazoles as inhibitors of bacterial DNA ligase

Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (308 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group L5V is 45.83% similar to enzyme product AMP

4cc6

Fragment-based discovery of 6 azaindazoles as inhibitors of bacterial DNA ligase

Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (308 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

4eeq

Crystal structure of e. Faecalis DNA ligase with inhibitor

Source: Enterococcus faecalis. Organism_taxid: 1351. Gene: liga, ef_0722

Chain: A (313 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

4efb

Crystal structure of DNA ligase

Source: Synthetic: yes. Enterococcus faecalis. Organism_taxid: 1351. Other_details: this sequence occurs naturally in bacterial

Chain: A (313 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

4efe

Crystal structure of DNA ligase

Source: Enterococcus faecalis. Organism_taxid: 1351

Chain: A (313 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

4glw

DNA ligase a in complex with inhibitor

Source: Streptococcus pneumoniae. Organism_taxid: 488223. Strain: p1031. Gene: liga, spp_1122. Expressed in: escherichia coli. Expression_system_taxid: 562

Chains: A, B (275 residues) CATH domain: 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

4glx

DNA ligase a in complex with inhibitor

Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: b2411, dnal, jw2403, lig, liga, lop, pdec. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (573 residues) CATH domains: 1.10.287.610 3.30.470.30 3.30.1490.70 2.40.50.140 6.20.10.30 1.10.150.20 1.10.150.20

4lh6

Crystal structure of a liga inhibitor

Source: Enterococcus faecalis. Organism_taxid: 226185. Strain: atcc 700802 / v583. Gene: liga, ef_0722. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (322 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

4lh7

Crystal structure of a liga inhibitor

Source: Enterococcus faecalis. Organism_taxid: 226185. Strain: atcc 700802 / v583. Gene: ef_0722, liga. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (321 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

4uco

Fragment bound to h.Influenza NAD dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (317 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

4ucr

Fragment bound to h.Influenza NAD dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (317 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group JCF is 40.74% similar to enzyme product AMP

4ucs

Fragment bound to h.Influenza NAD dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (317 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group 9MJ is 42.31% similar to enzyme product AMP

4uct

Fragment bound to h.Influenza NAD dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (318 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

4ucu

Fragment bound to h.Influenza NAD dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (318 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

4ucv

Fragment bound to h.Influenza NAD dependent DNA ligase

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (318 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

Bound ligand: Het Group I6G is 52.00% similar to enzyme product AMP

4ufz

Synthesis of novel NAD dependant DNA ligase inhibitors via negishi cross-coupling: development of sar and resistance studies

Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 562

Chain: A (317 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

5fpo

Structure of bacterial DNA ligase with small-molecule ligand 1h- indazol-7-amine (at4213) in an alternate binding site.

Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (306 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

5fpr

Structure of bacterial DNA ligase with small-molecule ligand pyrimidin-2-amine (at371) in an alternate binding site.

Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (307 residues) CATH domains: 1.10.287.610 3.30.1490.70 3.30.470.30

5tt5

Escherichia coli liga (k115m) in complex with NAD+

Source: Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: liga, dnal, lig, lop, pdec, b2411, jw2403. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Chain: A (581 residues)

Bound ligand: Het Group NAD corresponds to enzyme reactant NAD(+)

6kdu

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Atcc: 25618. Gene: liga. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768.

Chain: A (321 residues)

Bound ligand: Het Group AMP corresponds to enzyme product AMP

6kjm

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: liga. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Chain: A (321 residues)

Bound ligand: Het Group AMP corresponds to enzyme product AMP

6kkv

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: atcc 25618 / h37rv. Gene: liga, lig, rv3014c, mtv012.28c. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Chain: A (321 residues)

6krh

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: liga, lig, rv3014c, mtv012.28c. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Chain: A (321 residues)

Bound ligand: Het Group AMP corresponds to enzyme product AMP

6ksc

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: liga, lig, rv3014c, mtv012.28c. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Chain: A (321 residues)

Bound ligand: Het Group AMP corresponds to enzyme product AMP

6ksd

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: liga, lig, rv3014c, mtv012.28c. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Chain: A (321 residues)

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP

6lw8

Structural basis for domain rotation during adenylation of active site k123 and fragment library screening against NAD+ -dependent DNA ligase from mycobacterium tuberculosis

Source: Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: liga. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Chain: A (320 residues)

Bound ligand: Het Group EWO is 44.44% similar to enzyme product AMP

7k72

Structure of DNA ligase a from mycobacterium tuberculosis bound to nad

Source: Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: atcc 25618 / h37rv. Atcc: 25618. Gene: liga, lig, rv3014c, mtv012.28c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Chains: A, B, C, D (318 residues)

Bound ligand: Het Group NAD corresponds to enzyme reactant NAD(+)

8ak4

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

Source: Deinococcus radiodurans. Organism_taxid: 1299. Strain: atcc 13939 / dsm 20539 / jcm 16871 / lmg 4051 / nbrc 15346 / ncimb 9279 / r1 / vkm b-1422. Atcc: 13939. Gene: liga, dr_2069. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Expression_system_variant: de3 .

Chain: A (513 residues)

8jyd

A genetically encoded sensor based on a bacterial DNA ligase

Source: Enterococcus faecalis (strain atcc 700802 / v583). Organism_taxid: 226185. Gene: liga, ef_0722. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Chain: A (312 residues)

Bound ligand: Het Group NMN is 73.08% similar to enzyme product AMP