Structural and Functional Similarities of Prokaryotic and Eukaryotic DNA Polymerase Sliding Clamps

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1995 Sep 25

PMID 7478986

Citations 69

Authors

Z Kelman

M ODonnell

Affiliations

Soon will be listed here.

Abstract

The remarkable processivity of cellular replicative DNA polymerases derive their tight grip to DNA from a ring-shaped protein that encircles DNA and tethers the polymerase to the chromosome. The crystal structures of prototypical 'sliding clamps' of prokaryotes (beta subunit) and eukaryotes (PCNA) are ring shaped proteins for encircling DNA. Although beta is a dimer and PCNA is a trimer, their structures are nearly superimposable. Even though they are not hexamers, the sliding clamps have a pseudo 6-fold symmetry resulting from three globular domains comprising each beta monomer and two domains comprising each PCNA monomer. These domains have the same chain fold and are nearly identical in three-dimensions. The amino acid sequences of 11 beta and 13 PCNA proteins from different organisms have been aligned and studied to gain further insight into the relation between the structure and function of these sliding clamps. Furthermore, a putative embryonic form of PCNA is the size of beta and thus may encircle DNA as a dimer like the prokaryotic clamps.

Citing Articles

PCNA and Rnh1 independently participate in the protection of mitochondrial genome against UV-induced mutagenesis in yeast cells.

Latoszek M, Baginska-Drabiuk K, Sledziewska-Gojska E, Kaniak-Golik A Sci Rep. 2024; 14(1):31017.

PMID: 39730600 PMC: 11681198. DOI: 10.1038/s41598-024-82104-4.

Proliferating Cell Nuclear Antigen in the Era of Oncolytic Virotherapy.

Kwan A, Mcdermott-Brown I, Muthana M Viruses. 2024; 16(8).

PMID: 39205238 PMC: 11359830. DOI: 10.3390/v16081264.

PTBP1 plays an important role in the development of gastric cancer.

Chu Z, Zhu M, Luo Y, Hu Y, Feng X, Wang H Cancer Cell Int. 2023; 23(1):195.

PMID: 37670313 PMC: 10478210. DOI: 10.1186/s12935-023-03043-0.

From Processivity to Genome Maintenance: The Many Roles of Sliding Clamps.

Mulye M, Singh M, Jain V Genes (Basel). 2022; 13(11).

PMID: 36360296 PMC: 9690074. DOI: 10.3390/genes13112058.

Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice.

Belli G, Colomina N, Castells-Roca L, Lorite N J Fungi (Basel). 2022; 8(6).

PMID: 35736104 PMC: 9225081. DOI: 10.3390/jof8060621.

References

Skovgaard O . Nucleotide sequence of a Proteus mirabilis DNA fragment homologous to the 60K-rnpA-rpmH-dnaA-dnaN-recF-gyrB region of Escherichia coli. Gene. 1990; 93(1):27-34. DOI: 10.1016/0378-1119(90)90131-a. View

Leibovici M, Gusse M, Bravo R, Mechali M . Characterization and developmental expression of Xenopus proliferating cell nuclear antigen (PCNA). Dev Biol. 1990; 141(1):183-92. DOI: 10.1016/0012-1606(90)90113-w. View

SUZUKA I, Hata S, Matsuoka M, Kosugi S, Hashimoto J . Highly conserved structure of proliferating cell nuclear antigen (DNA polymerase delta auxiliary protein) gene in plants. Eur J Biochem. 1991; 195(2):571-5. DOI: 10.1111/j.1432-1033.1991.tb15739.x. View

Kodama H, Ito M, Ohnishi N, SUZUKA I, Komamine A . Molecular cloning of the gene for plant proliferating-cell nuclear antigen and expression of this gene during the cell cycle in synchronized cultures of Catharanthus roseus cells. Eur J Biochem. 1991; 197(2):495-503. DOI: 10.1111/j.1432-1033.1991.tb15937.x. View

Yamaguchi M, Hayashi Y, Hirose F, Matsuoka S, Moriuchi T, Shiroishi T . Molecular cloning and structural analysis of mouse gene and pseudogenes for proliferating cell nuclear antigen. Nucleic Acids Res. 1991; 19(9):2403-10. PMC: 329449. DOI: 10.1093/nar/19.9.2403. View

Hata S, Kouchi H, Tanaka Y, Minami E, Matsumoto T, SUZUKA I . Identification of carrot cDNA clones encoding a second putative proliferating cell-nuclear antigen, DNA polymerase delta auxiliary protein. Eur J Biochem. 1992; 203(3):367-71. DOI: 10.1111/j.1432-1033.1992.tb16559.x. View

Fujita M, Yoshikawa H, Ogasawara N . Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variations in the course of evolution. Gene. 1992; 110(1):17-23. DOI: 10.1016/0378-1119(92)90439-v. View

Gogol E, Young M, Kubasek W, Jarvis T, von Hippel P . Cryoelectron microscopic visualization of functional subassemblies of the bacteriophage T4 DNA replication complex. J Mol Biol. 1992; 224(2):395-412. DOI: 10.1016/0022-2836(92)91003-8. View

Lai C, Baumann P . Genetic analysis of an aphid endosymbiont DNA fragment homologous to the rnpA-rpmH-dnaA-dnaN-gyrB region of eubacteria. Gene. 1992; 113(2):175-81. DOI: 10.1016/0378-1119(92)90393-4. View

10.

Calcutt M, Schmidt F . Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome. J Bacteriol. 1992; 174(10):3220-6. PMC: 205989. DOI: 10.1128/jb.174.10.3220-3226.1992. View

11.

Kong X, Onrust R, ODonnell M, Kuriyan J . Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell. 1992; 69(3):425-37. DOI: 10.1016/0092-8674(92)90445-i. View

12.

Herendeen D, Kassavetis G, Geiduschek E . A transcriptional enhancer whose function imposes a requirement that proteins track along DNA. Science. 1992; 256(5061):1298-303. DOI: 10.1126/science.1598572. View

13.

Waseem N, Labib K, Nurse P, Lane D . Isolation and analysis of the fission yeast gene encoding polymerase delta accessory protein PCNA. EMBO J. 1992; 11(13):5111-20. PMC: 556989. DOI: 10.1002/j.1460-2075.1992.tb05618.x. View

14.

ODonnell M, Onrust R, Dean F, Chen M, Hurwitz J . Homology in accessory proteins of replicative polymerases--E. coli to humans. Nucleic Acids Res. 1993; 21(1):1-3. PMC: 309057. DOI: 10.1093/nar/21.1.1. View

15.

Reddy M, Weitzel S, von Hippel P . Assembly of a functional replication complex without ATP hydrolysis: a direct interaction of bacteriophage T4 gp45 with T4 DNA polymerase. Proc Natl Acad Sci U S A. 1993; 90(8):3211-5. PMC: 46269. DOI: 10.1073/pnas.90.8.3211. View

16.

Kuriyan J, ODonnell M . Sliding clamps of DNA polymerases. J Mol Biol. 1993; 234(4):915-25. DOI: 10.1006/jmbi.1993.1644. View

17.

Waga S, Hannon G, Beach D, Stillman B . The p21 inhibitor of cyclin-dependent kinases controls DNA replication by interaction with PCNA. Nature. 1994; 369(6481):574-8. DOI: 10.1038/369574a0. View

18.

Kelman Z, ODonnell M . DNA replication: enzymology and mechanisms. Curr Opin Genet Dev. 1994; 4(2):185-95. DOI: 10.1016/s0959-437x(05)80044-9. View

19.

Sanders G, Kassavetis G, Geiduschek E . Use of a macromolecular crowding agent to dissect interactions and define functions in transcriptional activation by a DNA-tracking protein: bacteriophage T4 gene 45 protein and late transcription. Proc Natl Acad Sci U S A. 1994; 91(16):7703-7. PMC: 44470. DOI: 10.1073/pnas.91.16.7703. View

20.

Flores-Rozas H, Kelman Z, Dean F, Pan Z, Harper J, Elledge S . Cdk-interacting protein 1 directly binds with proliferating cell nuclear antigen and inhibits DNA replication catalyzed by the DNA polymerase delta holoenzyme. Proc Natl Acad Sci U S A. 1994; 91(18):8655-9. PMC: 44665. DOI: 10.1073/pnas.91.18.8655. View