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UniProt functional annotation for Q9I1X7 | ||
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| UniProt code: Q9I1X7. |
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| Organism: | |
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1). |
| Taxonomy: | |
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas. |
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| Function: | |
With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'- ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'- phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide. {ECO:0000269|PubMed:15897197, ECO:0000269|PubMed:16046407, ECO:0000269|PubMed:20018881}. |
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| Function: | |
The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting. |
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| Catalytic activity: | |
Reaction=ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.; EC=6.5.1.1; |
| Cofactor: | |
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000305|PubMed:15520014, ECO:0000305|PubMed:15897197, ECO:0000305|PubMed:16046407, ECO:0000305|PubMed:16446439}; Note=Binds 4 Mn(2+); 2 Mn(2+) for polymerase/primase activity, 1 each for 3-phosphoesterase and ligase. {ECO:0000305|PubMed:15520014, ECO:0000305|PubMed:15897197, ECO:0000305|PubMed:16046407, ECO:0000305|PubMed:16446439}; |
| Activity regulation: | |
rNTP addition and end joining activities are stimulated by Ku homodimer. {ECO:0000269|PubMed:20018881}. |
| Subunit: | |
Monomer. Interacts with Ku (By similarity). {ECO:0000250}. |
| Domain: | |
The N-terminal 3'-phosphoesterase domain (PE) has 3'- ribonuclease and 3'-phosphatase activities. {ECO:0000269|PubMed:15897197}. |
| Domain: | |
The central ATP-dependent ligase domain (Lig) functions as an independent domain. {ECO:0000269|PubMed:15520014}. |
| Domain: | |
The C-terminal polymerase/primase domain (Pol) (PubMed:15520014) adds up to 4 rNTPs in a DNA template-directed fashion (PubMed:15897197). {ECO:0000269|PubMed:15520014, ECO:0000269|PubMed:15897197}. |
| Miscellaneous: | |
LigD has variable architecture; domain order can be permutated, domains can be independently encoded, while some bacteria lack the 3'-phosphoesterase domain entirely. |
| Similarity: | |
In the N-terminal section; belongs to the LigD 3'- phosphoesterase family. {ECO:0000305}. |
| Similarity: | |
In the central section; belongs to the ATP-dependent DNA ligase family. {ECO:0000305}. |
| Similarity: | |
In the C-terminal section; belongs to the LigD polymerase family. {ECO:0000305}. |
Annotations taken from UniProtKB at the EBI.