DB code: T00254

CATH domain 3.30.1490.70 : Dna Ligase; domain 1 Catalytic domain
2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P) Catalytic domain
3.30.470.30 : D-amino Acid Aminotransferase; Chain A, domain 1
E.C. 6.5.1.1
CSA 1a0i
M-CSA 1a0i
MACiE M0202

CATH domain Related DB codes (homologues)
2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P) M00220 M00186 T00050 D00291 D00294

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00969 DNA ligase
EC 6.5.1.1
Polydeoxyribonucleotide synthase [ATP]
NP_041963.1 (Protein)
NC_001604.1 (DNA/RNA sequence)
PF01068 (DNA_ligase_A_M)
[Graphical View]
O41026
A544R protein
NP_048900.1 (Protein)
NC_000852.5 (DNA/RNA sequence)
PF01068 (DNA_ligase_A_M)
[Graphical View]

KEGG enzyme name
deoxyribonucleic acid-joining enzyme
deoxyribonucleic repair enzyme
deoxyribonucleic joinase
deoxyribonucleic acid ligase
deoxyribonucleic acid joinase
deoxyribonucleic acid repair enzyme
DNA ligase (ATP)
polydeoxyribonucleotide synthase (ATP)
polynucleotide ligase
sealase
DNA repair enzyme
DNA joinase
DNA ligase
deoxyribonucleic ligase
deoxyribonucleate ligase
DNA-joining enzyme
deoxyribonucleic-joining enzyme

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00969 DNLI_BPT7 ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
O41026 O41026_PBCV1

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00039 C00039 C00046 C00046 C00020 C00013 C00039 C00046
E.C.
Compound Magnesium ATP (Deoxyribonucleotide)n (Deoxyribonucleotide)m (Ribonucleotide)n (Ribonucleotide)m AMP Pyrophosphate (Deoxyribonucleotide)n+m (Ribonucleotide)n+m
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide nucleic acids nucleic acids nucleic acids nucleic acids amine group,nucleotide phosphate group/phosphate ion nucleic acids nucleic acids
ChEBI 18420
15422
16027
29888
PubChem 888
5957
6083
1023
21961011
1a0iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:ATP Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fviA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-bound:AMP (bound to Lys27)
1a0iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fviA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1a0iA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fviA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1a0i & literature [1], [7] & [8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1a0iA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 34;LYS 238 ASP 36(divalent metal binding) mutant M2V
1fviA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 27;LYS 186 mutant D29A
1a0iA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 240
1fviA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 188
1a0iA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1fviA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.608, p.611-612
[2]
Fig.1 3
[7]
p.47, p.51-52, Fig.10 5
[8]

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID 96222302
PubMed ID 8653795
Journal Cell
Year 1996
Volume 85
Pages 607-15
Authors Subramanya HS, Doherty AJ, Ashford SR, Wigley DB
Title Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
Related PDB 1a0i
Related UniProtKB P00969
[2]
Resource
Comments
Medline ID
PubMed ID 8626651
Journal J Biol Chem
Year 1996
Volume 271
Pages 11083-9
Authors Doherty AJ, Ashford SR, Subramanya HS, Wigley DB
Title Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8646532
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 496
Authors Riddihough G
Title DNA ligase shows restraint.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9254695
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 3403-7
Authors Pritchard CE, Southern EM
Title Effects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9016621
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 727-34
Authors Sekiguchi J, Shuman S
Title Domain structure of vaccinia DNA ligase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9878388
Journal J Mol Biol
Year 1999
Volume 285
Pages 63-71
Authors Doherty AJ, Wigley DB
Title Functional domains of an ATP-dependent DNA ligase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10656817
Journal J Mol Biol
Year 2000
Volume 296
Pages 43-56
Authors Doherty AJ, Dafforn TR
Title Nick recognition by DNA ligases.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11106756
Journal Mol Cell
Year 2000
Volume 6
Pages 1183-93
Authors Odell M, Sriskanda V, Shuman S, Nikolov DB
Title Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
Related PDB 1fvi
Related UniProtKB

Comments

Created Updated
2004-03-25 2009-02-26