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| PROSITE documentation PDOC00295 |
ATP-dependent DNA ligase signatures and profile
Description:
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.
Last update:
April 2006 / Patterns revised.
Technical section:
PROSITE methods (with tools and information) covered by this documentation:
| DNA_LIGASE_A3, PS50160; ATP-dependent DNA ligase family profile (MATRIX) |
| Sequences known to belong to this class detected by the profile: |
ALL |
| Other sequence(s) detected in Swiss-Prot: |
1. |
|
|
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| Matching PDB structures:
1A0I 1VS0 1X9N 2CFM ... [ALL] |
| DNA_LIGASE_A1, PS00697; ATP-dependent DNA ligase AMP-binding site (PATTERN) |
| 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. |
|
|
|
| Matching PDB structures:
1A0I 1X9N 2CFM 2HIV ... [ALL] |
| DNA_LIGASE_A2, PS00333; ATP-dependent DNA ligase signature 2 (PATTERN) |
| Consensus pattern: |
E-G-[LIVMA]-[LIVM]-[LIVMA]-[KR]-x(5,8)-[YW]-[QNEKTI]-x(2,6)-[KRH]-x(3,5)-K-[LIVMFY]-K
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| 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. |
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|
| Matching PDB structures:
1A0I 2HIV 2HIX 3GDE ... [ALL] |
References:
| 1 |
Authors | Tomkinson A.E., Totty N.F., Ginsburg M., Lindahl T. |
| Title | Location of the active site for enzyme-adenylate formation in DNA ligases. |
| Source | Proc. Natl. Acad. Sci. U.S.A. 88:400-404(1991). |
| PubMed ID | 1988940 |
| 3 |
Authors | Kletzin A. |
| Title | Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. |
| Source | Nucleic Acids Res. 20:5389-5396(1992). |
| PubMed ID | 1437556 |
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