Replication factor A
Single-stranded binding protein. Stabilizes ssDNA in replication fork. Also involved in DNA repair and recombination.
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Rpa |
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Synonyms |
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Molecular weight |
•Heterotrimer: 70 kDa, 30 kDa, 14 KDa (Sc) |
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Biochemical properties |
•ssDNA binding ( high affinity), covers 20-30bp DNA but some what dependent on buffer (1) (2) Some dna compaction on binding, but not as much as E coli ssb (3)
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Motifs |
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Interactions |
Sc •cdc45/mcm2 /pole (4) mutual dependence for binding cdc45/rpa?? • Mcm10 (5) • rad51 (6) • rad52 (7) • pob subunit FACT (8) (9) (10) •Phosphorylated by Mec1 in response to DNA damage (11)
Xl •ku (12) • wrn (13) as FFA (in initiation phase replication)
Dm • Helicase (14)
Mammals •nucleolin (15) inhibitory happens after hs or genotoxic shock (16) (17) • mrn complex (18) • ercc (19) •various helicases (20) (21) (22) , • blm (23) • wrn (24) • XPA (25) • Pol d (26) •Brca2 (27)
Plant • viral replicator (28) |
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Modifications |
•2 stage modification in meiosis ime2 then mec1 (29) • hyperphosphorylation in hu (30) • up to 9 residues modified on genotoxic shock (31) |
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Structure |
• bound to DNA (32) (33) (34) (35) (36) • ss binding domains bound to DNA (37) • crystal structure 14/32 (38) |
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Cellular location and expression |
Xl •Component of pre-replication centres (39) •See increase in soluble rpa throughout S, no change bound. (40) .Suggest ORC is needed for binding. Binds before cdc45 (although others say after (41) does this represent different modes of binding?
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Other comments |
•Elongation lagging and leading strand synthesis- needs specific protein interactions not just ssDNA binding. Probably acts at multiple points (42) •Role in DNA repair: (43) (44) (45) (46) (47) () 48
Some part of this is in signalling – for 1 of the primary signals in repair pathways rpa/ss DNA complex allows loading of atrip and atr (49) 43. Some part of this is in signalling – for 1 of the primary signals in repair pathways rpa/ss DNA complex allows loading of atrip and atr (49) (50) (51) (52) (53) . May also have a related control role in normal xenopus cell cycle (54) (55) •Role in DNA recombination: (56) (57) (58) (59) •Role in transcription: (60) (61) (62) (63) (64) (65)
Sc •Must be present for loading pol alpha onto origins, (66) •Sld3 required for binding (67)
Sp •Needed for cut5 chromatin association (68) •needed to load 9-1-1 complex (69)
Xl •Must be present for loading pol alpha onto origins (70) • Mcm8 needed to load rpa onto replication forks ? (71) •Cdc7 required for binding (72) •Needed for cut5 chromatin association (73)
Dm
Mammals •Small amount found in pml bodies. (74) • alternative 30kDa subunit (75) •possible control of levels by PARP(76)
Archaea 1 subunit rpa (77)
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Rpa1 |
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Synonyms |
SpRad11 |
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Molecular weight |
•70Kda |
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Biochemical properties |
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Motifs |
•Zn finger (78) •multiple DNA binding sites (79) (80)
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Interactions |
Xl •Xripa/ importin b homologue ( though not for transport) (81)
Dm • CENP (82)
Mammals •Tag pola and vp16 (83) • Polymerase alpha and primase (2) • rad51/dmc (84) • p53 (85) (86) (87)
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Modifications |
Sc •Phosphorylated by Mec1 in response to DNA damage (11) •Phosphorylated (88)
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Structure |
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Cellular location and expression |
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Other comments |
• Alternative subunit in rice (89)
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Rpa2 |
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Synonyms |
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Molecular weight |
34 kDa |
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Biochemical properties |
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Motifs |
•DNA binding (79) |
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Interactions |
•Menin (90) •Rad52 (91)
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Modifications |
Sc •Phosphorylated during meiosis (92) • phosphorylated byMec1/3 (11) in both normal cell cycle and genotoxic stress (92) .In normal cell cycle modification is after the start of S and probably only chromatin bound that is modified (93)
Xenopus • in extracts dephosphorylated at end mitosis and binds to pre-replication centres. Phosphorylated form not chromatin bound in mitosis. (40) . Don’t see 2 forms present together. May be different in other species eg (4)
Mammals • Phosphorylated after association with ssDNA. (94) •Phosphorylated by cyclin A-CDK and DNA-PK (95) (96) – may be some obligate order in vitro •Chromatin associated Rpa2 is phosphorylated (93) •Hyperphosphorylated on DNA damage (97) (98) seems to be via DNApk (99) or ATM (100) (ie confusing) and in apoptosis (93)
Dm • phosphorylation multiple sites (101)
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Structure |
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Cellular location and expression |
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Other comments |
Mammals •Homologue reported rpa4 (rpa2) (75) Can interact with 1 and 3 but some find it separate from the other subunits (102) (103) , while others report always seen together (104) (105)
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Rpa3 |
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Synonyms |
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Molecular weight |
14 kDa (Sc) poorly conserved, eg 10 kDa (??); 8 kDa (Dm) |
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Biochemical properties |
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Motifs |
•DNA binding site (79) |
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Interactions |
Mammals •Ruv B homologue (106)
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Modifications |
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Structure |
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Cellular location and expression |
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Other comments |
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Revised |
13 Apr 08 |
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5. Ricke,R.M. and Bielinsky,A.K. (2004) Mcm10 regulates the stability and chromatin association of DNA polymerase-alpha. Mol Cell 16, 173-185.
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33. Bochkarev,A., Bochkareva,E., Frappier,L. and Edwards,A.M. (1999) The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J 18, 4498-4504.
34. Bochkareva,E., Korolev,S., Lees-Miller,S.P. and Bochkarev,A. (2002) Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J 21, 1855-1863.
35. Pfuetzner,R.A., Bochkarev,A., Frappier,L. and Edwards,A.M. (1997) Replication protein A. Characterization and crystallization of the DNA binding domain. J Biol Chem 272, 430-434.
36. Park,C.J., Lee,J.H. and Choi,B.S. (2005) Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen. Nucleic Acids Res 33, 4172-4181.
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49. You,Z., Kong,L. and Newport,J. (2002) The role of single-stranded DNA and polymerase alpha in establishing the ATR, Hus1 DNA replication checkpoint. J Biol Chem 277, 27088-27093.
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61. Li,R. and Botchan,M.R. (1993) The acidic transcriptional activation domains of VP16 and p53 bind the cellular replication protein A and stimulate in vitro BPV-1 DNA replication. Cell 73, 1207-1221.
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64. Bai,G., Norton,D.D., Prenger,M.S. and Kusiak,J.W. (1998) Single-stranded DNA-binding proteins and neuron-restrictive silencer factor participate in cell-specific transcriptional control of the NMDAR1 gene. J Biol Chem 273, 1086-1091.
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66. Tanaka,T. and Nasmyth,K. (1998) Association of RPA with chromosomal replication origins requires an Mcm protein, and is regulated by Rad53, and cyclin- and Dbf4-dependent kinases. EMBO J 17, 5182-5191.
67. Kamimura,Y., Tak,Y.S., Sugino,A. and Araki,H. (2001) Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae. EMBO J 20, 2097-2107.
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78. Kim,D.K., Stigger,E. and Lee,S.H. (1996) Role of the 70-kDa subunit of human replication protein A (I). Single-stranded dna binding activity, but not polymerase stimulatory activity, is required for DNA replication. J Biol Chem271, 15124-15129.
79. Philipova,D., Mullen,J.R., Maniar,H.S., Lu,J., Gu,C. and Brill,S.J. (1996) A hierarchy of SSB protomers in replication protein A. Genes Dev 10, 2222-2233.
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82. Perdigao,J., Logarinho,E., Avides,M.C. and Sunkel,C.E. (1999) Molecular cloning, developmental expression, and cellular localization of the 70-kDa RPA-1 subunit of Drosophila melanogaster. DNA Cell Biol 18, 923-936.
83. Braun,K.A., Lao,Y., He,Z., Ingles,C.J. and Wold,M.S. (1997) Role of protein-protein interactions in the function of replication protein A (RPA): RPA modulates the activity of DNA polymerase alpha by multiple mechanisms. Biochemistry 36, 8443-8454.
84. Golub,E.I., Gupta,R.C., Haaf,T., Wold,M.S. and Radding,C.M. (1998) Interaction of human rad51 recombination protein with single-stranded DNA binding protein, RPA. Nucleic Acids Res 26, 5388-5393.
85. Dutta,A., Ruppert,J.M., Aster,J.C. and Winchester,E. (1993) Inhibition of DNA replication factor RPA by p53. Nature 365, 79-82.
86. Miller,S.D., Moses,K., Jayaraman,L. and Prives,C. (1997) Complex formation between p53 and replication protein A inhibits the sequence-specific DNA binding of p53 and is regulated by single-stranded DNA. Mol Cell Biol 17, 2194-2201.
87. Abramova,N.A., Russell,J., Botchan,M. and Li,R. (1997) Interaction between replication protein A and p53 is disrupted after UV damage in a DNA repair-dependent manner. Proc Natl Acad Sci U S A 94, 7186-7191.
88. Nuss,J.E., Patrick,S.M., Oakley,G.G., Alter,G.M., Robison,J.G., Dixon,K. and Turchi,J.J. (2005) DNA damage induced hyperphosphorylation of replication protein A. 1. Identification of novel sites of phosphorylation in response to DNA damage. Biochemistry 44, 8428-8437.
89. Ishibashi,T., Kimura,S., Furukawa,T., Hatanaka,M., Hashimoto,J. and Sakaguchi,K. (2001) Two types of replication protein A 70 kDa subunit in rice, Oryza sativa: molecular cloning, characterization, and cellular & tissue distribution. Gene 272, 335-343.
90. Sukhodolets,K.E., Hickman,A.B., Agarwal,S.K., Sukhodolets,M.V., Obungu,V.H., Novotny,E.A., Crabtree,J.S., Chandrasekharappa,S.C., Collins,F.S., Spiegel,A.M., Burns,A.L. and Marx,S.J. (2003) The 32-kilodalton subunit of replication protein A interacts with menin, the product of the MEN1 tumor suppressor gene. Mol Cell Biol 23, 493-509.
91. Park,M.S., Ludwig,D.L., Stigger,E. and Lee,S.H. (1996) Physical interaction between human RAD52 and RPA is required for homologous recombination in mammalian cells. J Biol Chem 271, 18996-19000.
92. Brush,G.S., Clifford,D.M., Marinco,S.M. and Bartrand,A.J. (2001) Replication protein A is sequentially phosphorylated during meiosis. Nucleic Acids Res 29, 4808-4817.
93. Treuner,K., Findeisen,M., Strausfeld,U. and Knippers,R. (1999) Phosphorylation of replication protein A middle subunit (RPA32) leads to a disassembly of the RPA heterotrimer. J Biol Chem 274, 15556-15561.
94. Fotedar,R. and Roberts,J.M. (1992) Cell cycle regulated phosphorylation of RPA-32 occurs within the replication initiation complex. EMBO J 11, 2177-2187.
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