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Contents

Function

[PCNA_HUMAN] Proliferating Cell Nuclear Antigen (PCNA) is a protein that acts as a DNA sliding clamp. It forms a homotrimer encircling the DNA and binds other peptides means known as PCNA interacting proteins. It acts as a processivity factor for DNA polymerases and other enzymes which act upon DNA. Examples of such are DNA polymerase (Dpo) δ in eukaryotic cells[1]. The increases in processivity are very pronounced. The number of basepairs processed before complex dissociation occurs is increased more than a thousandfold (~10bp[2] to ~80kbp[3]) and the speed of nucleotide incorporation rises about a hundredfold [4].

Relevance

PCNA is featured in many cellular pathways involving DNA. FEN1 bound to PCNA acts as a flap endonuclease and cleaves a displaced ssDNA (flap) containing oxidatively damaged dideoxyribose residue [5]. As stated above PCNA is also vital to formation of the procesive complex for DNA replication [6] and is featured even in gene expression and transcription when bound to GADD45A [7]. Thus PCNA is relevant in research and even medicine.

PCNA is useful in the diagnosis of high-grade dysplasia[8].

Structural highlights

p15 regulates DNA replication and repair by binding to PCNA. PCNA-p15 peptide complex shows the peptide passes through the PCNA ring and has numerous interactions with it[9]. Of interest is the binding site contained at each face of the PCNA ring. Said site is formed by a C-terminal domain formed groove and an interdomain connecting loop (IDCL). Some partners do bind to the N-terminal domain as well. There are multiple PCNA interacting protein binding motifs, but the most common one is QxxΨxx∇∇ (where Ψ is a hydrophobic residue and ∇ is either the aromatic residue F or Y) [10][11] PCNA interacting protein binding pocket IDCL

Known mutations

S228I

hPCNA-S228I disorder tyr133 difference
hPCNA-S228I disorder tyr133 difference

A disease causing variant in human, which causes a large conformational change of the PCNA interacting protein binding pocket. While the overal structure of the S228I mutant is mostly similar to the wild type, the change causes displacements extending from the mutation site, which affect the IDCL. Notably Tyr133, a highly conservated residue, rotates outwards by nearly 90° to prevent spherical conflicts with Ile228. The changes cause the binding cavity of S228I to be about a third of the size of its wild type equivalent and makes it incompetent for PCNA interacting protein binding. Such changes, if they were permanent, would however be lethal, as the removal of PCNA-FEN1 interactions is lethal on its own [12]. While some client proteins (e.q. [[p21CIP1]]) are left relatively unaffected even in this state, others' binding energetics are hugely disrupted (e.q. RNase H2B or FEN1). The explaination for survival of an individual carrying this mutation is sufficient malleability of IDCL (and thus of PCNA itself). Thus a PCNA interacting protein might be able to initiate an "induced-fit". Even here the mutant is disadvantaged as the wild type has B-factors ~40% higher than the mutant. Thus the mutation negatively affects even the IDCL dynamics. [13]. See FEN1 bound to PCNA mutant.

Human PCNA S228I mutant secondary structure with marked mutation and rotated Tyr133 marked red in sequence. Helices are marked red, sheets green and loops blue. Note the IDCL region (residues around 125).
Human PCNA S228I mutant secondary structure with marked mutation and rotated Tyr133 marked red in sequence. Helices are marked red, sheets green and loops blue. Note the IDCL region (residues around 125).
Human PCNA interacting protein healthy binding site, IDCL marked blue
Human PCNA interacting protein healthy binding site, IDCL marked blue
hPCNA-S228I PCNA interacting protein binding site, IDCL marked blue
hPCNA-S228I PCNA interacting protein binding site, IDCL marked blue
Tyr 133 is rotated by ~90° due to spherical conflict with Ile 228 in human PCNA mutant S228I.
Tyr 133 is rotated by ~90° due to spherical conflict with Ile 228 in human PCNA mutant S228I.

Diseases

hPCNA-S228I disorder [14]

Symptoms resemble those of DNA damage and repair disorders (e.q. xenoderma pigmentosum). Among others heightened UV sensibility and deffects of nucleotide excission repair. DNA replication in patients seems to proceed close to the norm. While there have been observed similar disorder in yeast [15], their mechanism differs. The yeast diseases are caused by premature dissociation from DNA, while leaving PCNA interacting protein binding pocket unaffected. However there are two future avenues of research. The first is the aforementioned simillarity to xenoderma pigmentosum. XPG, a protein involved in the aforementioned disease, has a high level of sequence similarity in its PCNA binding motif to FEN1, a protein whose binding was shown to be disrupted by S228I. The second is the observed lack of interaction with RNase H2B thus intervening in the ribonucleotide excision repair pathway [16]

3D Structures of Proliferating Cell Nuclear Antigen

Proliferating cell nuclear antigen 3D structures


Human proliferating cell nuclear antigen trimer (cyan, green, deeppink) complex with p15 peptide (yellow, magenta) (PDB entry 4d2g)

Drag the structure with the mouse to rotate

Credits

Article created as an Structural biology of the cell assignment at the Faculty of Science, Charles University, Prague, Czech Republic.

Assignment author: Lukáš Cakl

References

  1. ↑ Duffy CM, Hilbert BJ, Kelch BA. A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site. J Mol Biol. 2016 Mar 27;428(6):1023-40. doi: 10.1016/j.jmb.2015.11.029. Epub 2015, Dec 11. PMID:26688547 doi:http://dx.doi.org/10.1016/j.jmb.2015.11.029
  2. ↑ Fay PJ, Johanson KO, McHenry CS, Bambara RA. Size classes of products synthesized processively by two subassemblies of Escherichia coli DNA polymerase III holoenzyme. J Biol Chem. 1982 May 25;257(10):5692-9. PMID:7040370
  3. ↑ Yao NY, Georgescu RE, Finkelstein J, O'Donnell ME. Single-molecule analysis reveals that the lagging strand increases replisome processivity but slows replication fork progression. Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13236-41. doi:, 10.1073/pnas.0906157106. Epub 2009 Aug 3. PMID:19666586 doi:http://dx.doi.org/10.1073/pnas.0906157106
  4. ↑ McInerney P, Johnson A, Katz F, O'Donnell M. Characterization of a triple DNA polymerase replisome. Mol Cell. 2007 Aug 17;27(4):527-38. doi: 10.1016/j.molcel.2007.06.019. PMID:17707226 doi:http://dx.doi.org/10.1016/j.molcel.2007.06.019
  5. ↑ Matsumoto Y, Kim K, Hurwitz J, Gary R, Levin DS, Tomkinson AE, Park MS. Reconstitution of proliferating cell nuclear antigen-dependent repair of apurinic/apyrimidinic sites with purified human proteins. J Biol Chem. 1999 Nov 19;274(47):33703-8. doi: 10.1074/jbc.274.47.33703. PMID:10559261 doi:http://dx.doi.org/10.1074/jbc.274.47.33703
  6. ↑ Lee SH, Hurwitz J. Mechanism of elongation of primed DNA by DNA polymerase delta, proliferating cell nuclear antigen, and activator 1. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5672-6. doi: 10.1073/pnas.87.15.5672. PMID:1974050 doi:http://dx.doi.org/10.1073/pnas.87.15.5672
  7. ↑ Sanchez R, Pantoja-Uceda D, Prieto J, Diercks T, Marcaida MJ, Montoya G, Campos-Olivas R, Blanco FJ. Solution structure of human growth arrest and DNA damage 45alpha (Gadd45alpha) and its interactions with proliferating cell nuclear antigen (PCNA) and Aurora A kinase. J Biol Chem. 2010 Jul 16;285(29):22196-201. Epub 2010 May 11. PMID:20460379 doi:10.1074/jbc.M109.069344
  8. ↑ Kullmann F, Fadaie M, Gross V, Knuchel R, Bocker T, Steinbach P, Scholmerich J, Ruschoff J. Expression of proliferating cell nuclear antigen (PCNA) and Ki-67 in dysplasia in inflammatory bowel disease. Eur J Gastroenterol Hepatol. 1996 Apr;8(4):371-9. PMID:8781908
  9. ↑ De Biasio A, de Opakua AI, Mortuza GB, Molina R, Cordeiro TN, Castillo F, Villate M, Merino N, Delgado S, Gil-Carton D, Luque I, Diercks T, Bernado P, Montoya G, Blanco FJ. Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair. Nat Commun. 2015 Mar 12;6:6439. doi: 10.1038/ncomms7439. PMID:25762514 doi:http://dx.doi.org/10.1038/ncomms7439
  10. ↑ doi: https://dx.doi.org/10.1016/S0092-8674(00)81347-1
  11. ↑ Bruning JB, Shamoo Y. Structural and thermodynamic analysis of human PCNA with peptides derived from DNA polymerase-delta p66 subunit and flap endonuclease-1. Structure. 2004 Dec;12(12):2209-19. PMID:15576034 doi:http://dx.doi.org/10.1016/j.str.2004.09.018
  12. ↑ Larsen E, Kleppa L, Meza TJ, Meza-Zepeda LA, Rada C, Castellanos CG, Lien GF, Nesse GJ, Neuberger MS, Laerdahl JK, William Doughty R, Klungland A. Early-onset lymphoma and extensive embryonic apoptosis in two domain-specific Fen1 mice mutants. Cancer Res. 2008 Jun 15;68(12):4571-9. doi: 10.1158/0008-5472.CAN-08-0168. PMID:18559501 doi:http://dx.doi.org/10.1158/0008-5472.CAN-08-0168
  13. ↑ Duffy CM, Hilbert BJ, Kelch BA. A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site. J Mol Biol. 2016 Mar 27;428(6):1023-40. doi: 10.1016/j.jmb.2015.11.029. Epub 2015, Dec 11. PMID:26688547 doi:http://dx.doi.org/10.1016/j.jmb.2015.11.029
  14. ↑ Duffy CM, Hilbert BJ, Kelch BA. A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site. J Mol Biol. 2016 Mar 27;428(6):1023-40. doi: 10.1016/j.jmb.2015.11.029. Epub 2015, Dec 11. PMID:26688547 doi:http://dx.doi.org/10.1016/j.jmb.2015.11.029
  15. ↑ Lau PJ, Flores-Rozas H, Kolodner RD. Isolation and characterization of new proliferating cell nuclear antigen (POL30) mutator mutants that are defective in DNA mismatch repair. Mol Cell Biol. 2002 Oct;22(19):6669-80. doi: 10.1128/mcb.22.19.6669-6680.2002. PMID:12215524 doi:http://dx.doi.org/10.1128/mcb.22.19.6669-6680.2002
  16. ↑ Reijns MA, Rabe B, Rigby RE, Mill P, Astell KR, Lettice LA, Boyle S, Leitch A, Keighren M, Kilanowski F, Devenney PS, Sexton D, Grimes G, Holt IJ, Hill RE, Taylor MS, Lawson KA, Dorin JR, Jackson AP. Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell. 2012 May 25;149(5):1008-22. doi: 10.1016/j.cell.2012.04.011. Epub 2012 May , 10. PMID:22579044 doi:http://dx.doi.org/10.1016/j.cell.2012.04.011

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