EzCatDB: T00254

DB codeT00254
CATH domainDomain 13.30.1490.70Catalytic domain
Domain 22.40.50.140Catalytic domain
Domain 33.30.470.30
E.C.6.5.1.1
CSA1a0i
MACiEM0202

CATH domainRelated DB codes (homologues)
2.40.50.140M00220,M00186,T00050,D00291,D00294

Enzyme Name
Swiss-protKEGG

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


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

Subcellular location

Cofactor



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
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 Swiss-protP00969
[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
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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