PROSITE documentation PDOC00295

{PDOC00295}
{PS00697; DNA_LIGASE_A1}
{PS00333; DNA_LIGASE_A2}
{PS50160; DNA_LIGASE_A3}
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* ATP-dependent DNA ligase signatures and profile *
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DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA
fragments by catalyzing the formation of an internucleotide ester bond between
phosphate and deoxyribose. It is active during DNA replication, DNA repair and
DNA recombination.  There  are  two  forms  of  DNA  ligase:  one requires ATP
(EC 6.5.1.1), the other NAD (EC 6.5.1.2).

Eukaryotic, archaebacterial,  virus  and  phage DNA ligases are ATP-dependent.
During the  first  step of the joining reaction, the ligase interacts with ATP
to form  a  covalent enzyme-adenylate intermediate. A conserved lysine residue
is the site of adenylation [1,2].

Apart from the active  site  region,  the  only conserved region common to all
ATP-dependent DNA ligases is found [3] in the C-terminal section and  contains
a conserved glutamate as well as four positions with conserved basic residues.

We developed signature patterns for both conserved regions.

-Consensus pattern: [EDQH]-{K}-K-{VEDI}-[DN]-G-{GLYN}-R-[GACIVM]
                    [K is the active site residue]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: 33.

-Consensus pattern: E-G-[LIVMA]-[LIVM]-[LIVMA]-[KR]-x(5,8)-[YW]-[QNEKTI]-
                    x(2,6)-[KRH]-x(3,5)-K-[LIVMFY]-K
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for archebacterial DNA ligases.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: 1.

-Last update: April 2006 / Patterns revised.

[ 1] Tomkinson A.E., Totty N.F., Ginsburg M., Lindahl T.
     "Location of the active site for enzyme-adenylate formation in DNA
     ligases."
     Proc. Natl. Acad. Sci. U.S.A. 88:400-404(1991).
     PubMed=1988940
[ 2] Lindahl T., Barnes D.E.
     "Mammalian DNA ligases."
     Annu. Rev. Biochem. 61:251-281(1992).
     PubMed=1497311; DOI=10.1146/annurev.bi.61.070192.001343
[ 3] Kletzin A.
     "Molecular characterisation of a DNA ligase gene of the extremely
     thermophilic archaeon Desulfurolobus ambivalens shows close
     phylogenetic relationship to eukaryotic ligases."
     Nucleic Acids Res. 20:5389-5396(1992).
     PubMed=1437556

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