241 human active and 13 inactive phosphatases in total;
194 phosphatases have substrate data;
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336 protein substrates;
83 non-protein substrates;
1215 dephosphorylation interactions;
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299 KEGG pathways;
876 Reactome pathways;
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last scientific update: 11 Mar, 2019
last maintenance update: 01 Sep, 2023
Cytoplasm Nucleus Note=Partially colocalizes with PCNAand POLD1 at S phase replication sites (PubMed:11595739)Recruited to DNA damage sites within 2 hours following UVirradiation (PubMed:20227374, PubMed:22801543)
Function (UniProt annotation)
As a component of the trimeric and tetrameric DNApolymerase delta complexes (Pol-delta3 and Pol-delta4,respectively), plays a role in high fidelity genome replication,including in lagging strand synthesis, and repair Required foroptimal Pol-delta activity Stabilizes the Pol-delta complex andplays a major role in Pol-delta stimulation by PCNA(PubMed:10219083, PubMed:10852724, PubMed:11595739,PubMed:16510448, PubMed:24035200) Pol-delta3 and Pol-delta4 arecharacterized by the absence or the presence of POLD4 Theyexhibit differences in catalytic activity Most notably, Pol-delta3 shows higher proofreading activity than Pol-delta4(PubMed:19074196, PubMed:20334433) Although both Pol-delta3 andPol-delta4 process Okazaki fragments in vitro, Pol-delta3 may alsobe better suited to fulfill this task, exhibiting near-absence ofstrand displacement activity compared to Pol-delta4 and stallingon encounter with the 5'-blocking oligonucleotides Pol-delta3idling process may avoid the formation of a gap, while maintaininga nick that can be readily ligated (PubMed:24035200) Along withDNA polymerase kappa, DNA polymerase delta carries outapproximately half of nucleotide excision repair (NER) synthesisfollowing UV irradiation In this context, POLD3, along with PCNAand RFC1-replication factor C complex, is required to recruitPOLD1, the catalytic subunit of the polymerase delta complex, toDNA damage sites (PubMed:20227374) Under conditions of DNAreplication stress, required for the repair of broken replicationforks through break-induced replication (BIR) (PubMed:24310611)Involved in the translesion synthesis (TLS) of templates carryingO6-methylguanine or abasic sites performed by Pol-delta4,independently of DNA polymerase zeta (REV3L) or eta (POLH)Facilitates abasic site bypass by DNA polymerase delta bypromoting extension from the nucleotide inserted opposite thelesion (PubMed:19074196, PubMed:25628356, PubMed:27185888) Alsoinvolved in TLS, as a component of the POLZ complex Along withPOLD2, dramatically increases the efficiency and processivity ofDNA synthesis of the minimal DNA polymerase zeta complex,consisting of only REV3L and REV7 (PubMed:24449906)
A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (DnaB or MCM complex) precedes the DNA synthetic machinery and unwinds the duplex parental DNA in cooperation with the SSB or RPA. On the leading strand, replication occurs continuously in a 5 to 3 direction, whereas on the lagging strand, DNA replication occurs discontinuously by synthesis and joining of short Okazaki fragments. In prokaryotes, the leading strand replication apparatus consists of a DNA polymerase (pol III core), a sliding clamp (beta), and a clamp loader (gamma delta complex). The DNA primase (DnaG) is needed to form RNA primers. Normally, during replication of the lagging-strand DNA template, an RNA primer is removed either by an RNase H or by the 5 to 3 exonuclease activity of DNA pol I, and the DNA ligase joins the Okazaki fragments. In eukaryotes, three DNA polymerases (alpha, delta, and epsilon) have been identified. DNA primase forms a permanent complex with DNA polymerase alpha. PCNA and RFC function as a clamp and a clamp loader. FEN 1 and RNase H1 remove the RNA from the Okazaki fragments and DNA ligase I joins the DNA.
Base excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair initiated by lesion-specific DNA glycosylases and completed by either of the two sub-pathways: short-patch BER where only one nucleotide is replaced and long-patch BER where 2-13 nucleotides are replaced. Each sub-pathway of BER relies on the formation of protein complexes that assemble at the site of the DNA lesion and facilitate repair in a coordinated fashion. This process of complex formation appears to provide an increase in specificity and efficiency to the BER pathway, thereby facilitating the maintenance of genome integrity by preventing the accumulation of highly toxic repair intermediates.
Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the NER pathway are linked to at least three diseases: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The repair of damaged DNA involves at least 30 polypeptides within two different sub-pathways of NER known as transcription-coupled repair (TCR-NER) and global genome repair (GGR-NER). TCR refers to the expedited repair of lesions located in the actively transcribed strand of genes by RNA polymerase II (RNAP II). In GGR-NER the first step of damage recognition involves XPC-hHR23B complex together with XPE complex (in prokaryotes, uvrAB complex). The following steps of GGR-NER and TCR-NER are similar.
DNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication, thereby preventing mutations from becoming permanent in dividing cells. MMR also suppresses homologous recombination and was recently shown to play a role in DNA damage signaling. Defects in MMR are associated with genome-wide instability, predisposition to certain types of cancer including HNPCC, resistance to certain chemotherapeutic agents, and abnormalities in meiosis and sterility in mammalian systems.The Escherichia coli MMR pathway has been extensively studied and is well characterized. In E. coli, the mismatch-activated MutS-MutL-ATP complex licenses MutH to incise the nearest unmethylated GATC sequence. UvrD and an exonuclease generate a gap. This gap is filled by pol III and DNA ligase. The GATC sites are then methylated by Dam. Several human MMR proteins have been identified based on their homology to E. coli MMR proteins. These include human homologs of MutS and MutL. Although E. coli MutS and MutL proteins are homodimers, human MutS and MutL homologs are heterodimers. The role of hemimethylated dGATC sites as a signal for strand discrimination is not conserved from E. coli to human. Human MMR is presumed to be nick-directed in vivo, and is thought to discriminate daughter and template strands using a strand-specific nick.
Homologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs), potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves the generation of a single-stranded region of DNA, followed by strand invasion, formation of a Holliday junction, DNA synthesis using the intact strand as a template, branch migration and resolution. It is investigated that RecA/Rad51 family proteins play a central role. The breast cancer susceptibility protein Brca2 and the RecQ helicase BLM (Bloom syndrome mutated) are tumor suppressors that maintain genome integrity, at least in part, through HR.
Human T-cell leukemia virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammatory diseases such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Expression of Tax, a viral regulatory protein is critical to the pathogenesis. Tax is a transcriptional co-factor that interfere several signaling pathways related to anti-apoptosis or cell proliferation. The modulation of the signaling by Tax involve its binding to transcription factors like CREB/ATF, NF-kappa B, SRF, and NFAT.
Damaged double strand DNA (dsDNA) cannot be successfully used as a template by replicative DNA polymerase delta (POLD) and epsilon (POLE) complexes (Hoege et al. 2002). When the replication complex composed of PCNA, RPA, RFC and POLD or POLE stalls at a DNA damage site, PCNA becomes monoubiquitinated by RAD18 bound to UBE2B (RAD6). POLD or POLE dissociate from monoubiquitinated PCNA, while Y family DNA polymerases - REV1, POLH (DNA polymerase eta), POLK (DNA polymerase kappa) and POLI (DNA polymerase iota) - bind monoubiquitinated PCNA through their ubiquitin binding and PCNA binding motifs, resulting in a polymerase switch and initiation of translesion synthesis (TLS) (Hoege et al. 2002, Friedberg et al. 2005)
After the primers are synthesized on the G-Rich strand, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a \sliding clamp\structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA
Once polymerase switching from pol alpha to pol delta is complete the processive synthesis of a short run of DNA called an Okazaki fragment begins. DNA synthesis is discontinuous and as the extending Okazaki fragment reaches the RNA primer, this primer is folded into a single-stranded flap, which is removed by endonucleases. The process of extension is completed by the ligation of adjacent Okazaki fragments
Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase
Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap (Tsurimoto et al.1991)
MSH2:MSH6 (MutSalpha) binds single base mismatches and unpaired loops of 1-2 nucleotides (reviewed in Edelbrock et al. 2013). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta), which mediates repair of larger mismatches, and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). The MSH6 subunit is responsible for binding the mismatch, which activates MSH2:MSH6 to exchange ADP for ATP, adopt the conformation to allow movement on the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 has endonucleolytic activity and makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I
MSH2:MSH3 (MutSbeta) binds unpaired loops of 2 or more nucleotides (Palombo et al. 1996, Genschel et al. 1998). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta) and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). Binding of the mismatch activates MSH2:MSH3 to exchange ADP for ATP, adopt the conformation to allow movement along the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I
Long-patch base excision repair (BER) can proceed through PCNA-dependent DNA strand displacement synthesis by replicative DNA polymerases - DNA polymerase delta complex (POLD) or DNA polymerase epsilon (POLE) complex. The PCNA-dependent branch of long-patch BER may occur in cells in the S phase of the cell cycle, when the replication complexes that contain PCNA, POLD or POLE, RPA and RFC are available. POLB incorporates the first nucleotide at the 3'-end of APEX1-generated single strand break (SSB), thus displacing the damaged AP (abasic) dideoxyribose phosphate residue at the 5'-end of SSB (5'ddRP). PCNA is recruited to BER sites by APEX1 and flap endonuclease FEN1, and loaded onto damaged DNA by RFC. POLD and POLE in complex with PCNA continue the displacement DNA strand synthesis. FEN1 cleaves the displaced DNA strand with the AP residue (5'ddRP), and DNA ligase I (LIG1) ligates the multiple nucleotide patch at the 3' end of the SSB with the FEN1-processed 5'-end of the SSB (Klungland and Lindahl 1997, Stucki et al. 1998, Dianov et al. 1999, Matsumoto et al. 1999, Podlutsky et al. 2001, Dianova et al. 2001, Ranalli et al. 2002)
The initiation and extent of translesion DNA synthesis (TLS) has to be tightly controlled in order to limit TLS-induced mutagenesis, caused by the low fidelity of TLS-participating DNA polymerases. Since monoubiquitination of PCNA at lysine residue K164 is a prerequisite for the assembly of TLS complexes on damaged DNA templates, PCNA deubiquitination is a key step in TLS termination that allows DNA polymerase switching from Y family DNA polymerases involved in TLS to replicative DNA polymerases delta and epsilon (Povlsen et al. 2012, Park et al. 2014)
Homology directed repair (HDR) through homologous recombination is known as homologous recombination repair (HRR). HRR occurs after extensive resection of DNA double strand break (DSB) ends, which creates long 3'-ssDNA overhangs. RAD51 coats 3'-ssDNA overhangs in a BRCA2-controlled fashion, creating invasive RAD51 nucleofilaments. The RAD51 nucleofilament invades a sister chromatid DNA duplex, leading to D-loop formation. After the D-loop is extended by DNA repair synthesis, the resulting recombination intermediates in the form of extended D-loops or double Holliday junctions can be resolved through crossover- or non-crossover-generating processes (reviewed by Ciccia and Elledge 2010)
Global genome nucleotide excision repair (GG-NER) is completed by DNA repair synthesis that fills the single stranded gap created after dual incision of the damaged DNA strand and excision of the ~27-30 bases long oligonucleotide that contains the lesion. DNA synthesis is performed by DNA polymerases epsilon or delta, or the Y family DNA polymerase kappa (POLK), which are loaded to the repair site after 5' incision (Staresincic et al. 2009, Ogi et al. 2010). DNA ligases LIG1 or LIG3 (as part of the LIG3:XRCC1 complex) ligate the newly synthesized stretch of oligonucleotides to the incised DNA strand (Moser et al. 2007)
Double incision at the damaged DNA strand excises the oligonucleotide that contains the lesion from the open bubble. The excised oligonucleotide is ~27-30 bases long. Incision 5' to the damage site, by ERCC1:ERCC4 endonuclease, precedes the incision 3' to the damage site by ERCC5 endonuclease (Staresincic et al. 2009)
In transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), the oligonucleotide that contains the lesion is excised from the open bubble structure via dual incision of the affected DNA strand. 5' incision by the ERCC1:ERCC4 (ERCC1:XPF) endonuclease precedes 3' incision by ERCC5 (XPG) endonuclease. In order for the TC-NER pre-incision complex to assemble and the endonucleases to incise the damaged DNA strand, the RNA polymerase II (RNA Pol II) complex has to backtrack - reverse translocate from the damage site. Although the mechanistic details of this process are largely unknown in mammals, it may involve ERCC6/ERCC8-mediated chromatin remodelling/ubiquitination events, the DNA helicase activity of the TFIIH complex and TCEA1 (TFIIS)-stimulated cleavage of the 3' protruding end of nascent mRNA by RNA Pol II (Donahue et al. 1994, Lee et al. 2002, Sarker et al. 2005, Vermeulen and Fousteri 2013, Hanawalt and Spivak 2008, Staresincic et al. 2009, Epshtein et al. 2014)
In transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), DNA polymerases delta or epsilon, or the Y family DNA polymerase kappa, fill in the single stranded gap that remains after dual incision. DNA ligases LIG1 or LIG3, the latter in complex with XRCC1, subsequently seal the single stranded nick by ligating the 3' end of the newly synthesized patch with the 5' end of incised DNA (Moser et al. 2007, Staresincic et al. 2009, Ogi et al. 2010)
After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a \sliding clamp\structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA
Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap (Tsurimoto et al.1991)
The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a single-stranded flap, which is removed by endonucleases. This is followed by the ligation of adjacent Okazaki fragments
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, FRET, Far Western, Protein-peptide, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, confocal microscopy, far western blotting, fluorescent resonance energy transfer, isothermal titration calorimetry, x-ray crystallography
association, colocalization, direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, anti tag coimmunoprecipitation, chromatography technology, cosedimentation through density gradient, ion exchange chromatography, molecular sieving
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, FRET, Far Western, Protein-peptide, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, confocal microscopy, far western blotting, fluorescent resonance energy transfer, isothermal titration calorimetry, x-ray crystallography
association, colocalization, direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, anti tag coimmunoprecipitation, chromatography technology, cosedimentation through density gradient, ion exchange chromatography, molecular sieving
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, FRET, Far Western, Protein-peptide, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, confocal microscopy, far western blotting, fluorescent resonance energy transfer, isothermal titration calorimetry, x-ray crystallography
association, colocalization, direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, anti tag coimmunoprecipitation, chromatography technology, cosedimentation through density gradient, ion exchange chromatography, molecular sieving
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