polynucleotide 3'-phosphatase [Saccharomyces cerevisiae S288C]
Protein Classification
HAD family hydrolase( domain architecture ID 229399)
HAD (haloacid dehalogenase) family hydrolase; the HAD family includes phosphoesterases, ATPases, phosphonatases, dehalogenases, and sugar phosphomutases acting on a remarkably diverse set of substrates
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| HAD_like super family | cl21460 | Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes ... |
30-236 | 5.77e-66 | ||||
Haloacid Dehalogenase-like Hydrolases; The haloacid dehalogenase (HAD) superfamily includes carbon and phosphorus hydrolases such as 2-haloalkonoate dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, among others. These proteins catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a conserve alpha/beta core domain, and many also possess a small cap domain, with varying folds and functions. The actual alignment was detected with superfamily member cd01625: Pssm-ID: 473868 Cd Length: 154 Bit Score: 201.04 E-value: 5.77e-66
|
||||||||
| Name | Accession | Description | Interval | E-value | ||||
| HAD_PNP | cd01625 | polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional ... |
30-236 | 5.77e-66 | ||||
polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional enzyme polynucleotide 5'-kinase/3'-phosphatase; Polynucleotide 3'-phosphatase (PNP) domain. This domain dephosphorylates single-stranded as well as double-stranded 3'-phospho termini. It is found in bifunctional enzyme polynucleotide kinase/phosphatase (PNKP) which contain both kinase and phosphatase domains. PNKP plays a key role in both base excision repair and non-homologous end-joining DNA repair pathway. DNA strand breaks can result from DNA damage by ionizing radiation and chemical agents, such as alkylating agents or anticancer agents. Such DNA damage often results in DNA strands with 5'-hydroxyl and 3'-phosphate termini. However, the repair of DNA damage by DNA polymerases and ligases requires 5'-phosphate and 3'-hydroxyl termini. PNKP acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319766 Cd Length: 154 Bit Score: 201.04 E-value: 5.77e-66
|
||||||||
| DNA-3'-Pase | TIGR01664 | DNA 3'-phosphatase; This model represents a family of proteins and protein domains which ... |
11-237 | 5.53e-63 | ||||
DNA 3'-phosphatase; This model represents a family of proteins and protein domains which catalyze the dephosphorylation of DNA 3'-phosphates. It is believed that this activity is important for the repair of single-strand breaks in DNA caused by radiation or oxidative damage. This domain is often (TIGR01663), but not always linked to a DNA 5'-kinase domain. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region. Pssm-ID: 211680 Cd Length: 166 Bit Score: 194.21 E-value: 5.53e-63
|
||||||||
| PNK3P | pfam08645 | Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the ... |
30-236 | 1.03e-50 | ||||
Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin. Pssm-ID: 370030 Cd Length: 161 Bit Score: 162.43 E-value: 1.03e-50
|
||||||||
| Name | Accession | Description | Interval | E-value | ||||
| HAD_PNP | cd01625 | polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional ... |
30-236 | 5.77e-66 | ||||
polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional enzyme polynucleotide 5'-kinase/3'-phosphatase; Polynucleotide 3'-phosphatase (PNP) domain. This domain dephosphorylates single-stranded as well as double-stranded 3'-phospho termini. It is found in bifunctional enzyme polynucleotide kinase/phosphatase (PNKP) which contain both kinase and phosphatase domains. PNKP plays a key role in both base excision repair and non-homologous end-joining DNA repair pathway. DNA strand breaks can result from DNA damage by ionizing radiation and chemical agents, such as alkylating agents or anticancer agents. Such DNA damage often results in DNA strands with 5'-hydroxyl and 3'-phosphate termini. However, the repair of DNA damage by DNA polymerases and ligases requires 5'-phosphate and 3'-hydroxyl termini. PNKP acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Pssm-ID: 319766 Cd Length: 154 Bit Score: 201.04 E-value: 5.77e-66
|
||||||||
| DNA-3'-Pase | TIGR01664 | DNA 3'-phosphatase; This model represents a family of proteins and protein domains which ... |
11-237 | 5.53e-63 | ||||
DNA 3'-phosphatase; This model represents a family of proteins and protein domains which catalyze the dephosphorylation of DNA 3'-phosphates. It is believed that this activity is important for the repair of single-strand breaks in DNA caused by radiation or oxidative damage. This domain is often (TIGR01663), but not always linked to a DNA 5'-kinase domain. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region. Pssm-ID: 211680 Cd Length: 166 Bit Score: 194.21 E-value: 5.53e-63
|
||||||||
| PNK3P | pfam08645 | Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the ... |
30-236 | 1.03e-50 | ||||
Polynucleotide kinase 3 phosphatase; Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin. Pssm-ID: 370030 Cd Length: 161 Bit Score: 162.43 E-value: 1.03e-50
|
||||||||
| PNK-3'Pase | TIGR01663 | polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5 ... |
31-238 | 6.45e-09 | ||||
polynucleotide 5'-kinase 3'-phosphatase; This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78 Pssm-ID: 130724 [Multi-domain] Cd Length: 526 Bit Score: 55.42 E-value: 6.45e-09
|
||||||||
| Blast search parameters | ||||
|
