EzCatDB: T00254
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DB codeT00254
CATH domainDomain 13.30.1490.70 : Dna Ligase; domain 1Catalytic domain
Domain 22.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)Catalytic domain
Domain 33.30.470.30 : D-amino Acid Aminotransferase; Chain A, domain 1
E.C.6.5.1.1
CSA1a0i
MACiEM0202

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

Enzyme Name
UniProtKBKEGG

P00969O41026
Protein nameDNA ligase
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
deoxyribonucleic acid-joining enzyme
deoxyribonucleic repair enzyme
deoxyribonucleic joinase
deoxyribonucleic acid ligase
deoxyribonucleic acid joinase
deoxyribonucleic acid repair enzyme
SynonymsEC 6.5.1.1
Polydeoxyribonucleotide synthase [ATP]
A544R protein
RefSeqNP_041963.1 (Protein)
NC_001604.1 (DNA/RNA sequence)
NP_048900.1 (Protein)
NC_000852.5 (DNA/RNA sequence)
PfamPF01068 (DNA_ligase_A_M)
[Graphical view]
PF01068 (DNA_ligase_A_M)
[Graphical view]


UniProtKB:Accession NumberP00969O41026
Entry nameDNLI_BPT7O41026_PBCV1
ActivityATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Subunit

Subcellular location

Cofactor


Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C00039C00039C00046C00046C00020C00013C00039C00046
CompoundMagnesiumATP(Deoxyribonucleotide)n(Deoxyribonucleotide)m(Ribonucleotide)n(Ribonucleotide)mAMPPyrophosphate(Deoxyribonucleotide)n+m(Ribonucleotide)n+m
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidenucleic acidsnucleic acidsnucleic acidsnucleic acidsamine group,nucleotidephosphate group/phosphate ionnucleic acidsnucleic acids
ChEBI18420
15422




16027
29888



PubChem888
5957




6083
21961011
1023



                   
1a0iA01UnboundBound:ATPUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fviA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:AMP(bound to Lys27)
1a0iA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fviA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1a0iA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fviA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:SO4UnboundUnboundUnbound

Active-site residues
resource
PDB;1a0i & literature [1], [7] & [8]
pdbCatalytic residuesCofactor-binding residuescomment
           
1a0iA01LYS 34;LYS 238
ASP 36(divalent metal binding)
mutant M2V
1fviA01LYS 27;LYS 186
                              
mutant D29A
1a0iA02LYS 240
 
 
1fviA02LYS 188
 
 
1a0iA03 
 
 
1fviA03 
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.608, p.611-612
[2]Fig.13
[7]p.47, p.51-52, Fig.105
[8]


references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID96222302
PubMed ID8653795
JournalCell
Year1996
Volume85
Pages607-15
AuthorsSubramanya HS, Doherty AJ, Ashford SR, Wigley DB
TitleCrystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
Related PDB1a0i
Related UniProtKBP00969
[2]
PubMed ID8626651
JournalJ Biol Chem
Year1996
Volume271
Pages11083-9
AuthorsDoherty AJ, Ashford SR, Subramanya HS, Wigley DB
TitleBacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization.
[3]
PubMed ID8646532
JournalNat Struct Biol
Year1996
Volume3
Pages496
AuthorsRiddihough G
TitleDNA ligase shows restraint.
[4]
PubMed ID9254695
JournalNucleic Acids Res
Year1997
Volume25
Pages3403-7
AuthorsPritchard CE, Southern EM
TitleEffects of base mismatches on joining of short oligodeoxynucleotides by DNA ligases.
[5]
PubMed ID9016621
JournalNucleic Acids Res
Year1997
Volume25
Pages727-34
AuthorsSekiguchi J, Shuman S
TitleDomain structure of vaccinia DNA ligase.
[6]
PubMed ID9878388
JournalJ Mol Biol
Year1999
Volume285
Pages63-71
AuthorsDoherty AJ, Wigley DB
TitleFunctional domains of an ATP-dependent DNA ligase.
[7]
PubMed ID10656817
JournalJ Mol Biol
Year2000
Volume296
Pages43-56
AuthorsDoherty AJ, Dafforn TR
TitleNick recognition by DNA ligases.
[8]
PubMed ID11106756
JournalMol Cell
Year2000
Volume6
Pages1183-93
AuthorsOdell M, Sriskanda V, Shuman S, Nikolov DB
TitleCrystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.
Related PDB1fvi


createdupdated
2004-03-252009-02-26


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