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Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA

¹ Department of Structural Biology and
² Department of Molecular Biology, Biomolecular Engineering Research Institute, Osaka 565-0874, Japan

Reprint requests to: Kosuke Morikawa, Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan; e-mail: morikawa{at}beri.or.jp; fax: 81-6-6872-8219.

(RECEIVED September 27, 2002; FINAL REVISION January 2, 2003; ACCEPTED January 14, 2003)

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.0234503.

³ Present address: Pharmaceutical Research Institute, Kyowa Hakko Kogyo Co. Ltd., 1188, Shimatogari, Nagaizumi-cho, Sunto-gun, Shizuoka 411-8731, Japan.

⁴ Present address: Laboratory of Protein Chemistry and Engineering, Faculty of Agriculture, Kyushu University, Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812–8581, Japan.

	Abstract

TOP Abstract Introduction Results Discussion Materials and methods References

 
Two mutant proliferating cell nuclear antigens from the hyperthermophilic archaeon Pyrococcus furiosus, PfuPCNA(D143A) and PfuPCNA(D143A/D147A), were prepared by site-specific mutagenesis. The results from gel filtration showed that mutations at D143 and D147 drastically affect the stability of the trimeric structure of PfuPCNA. The PfuPCNA(D143A) still retained the activity to stimulate the DNA polymerase reaction, but PfuPCNA(D143A/D147A) lost the activity. Crystal structures of the mutant PfuPCNAs were determined. Although the wild-type PCNA forms a toroidal trimer with intermolecular hydrogen bonds between the N- and C-terminal domains, the mutant PfuPCNAs exist as V-shaped dimers through intermolecular hydrogen bonds between the two C-terminal domains in the crystal. Because the mutated residues are involved in the intermolecular ion pairs through their side chains in the wild-type PfuPCNA, these ion pairs seem to play a key role in maintaining the toroidal structure of the PfuPCNA trimer. The comparison of the crystal structures revealed intriguing conformational flexibility of each domain in the PfuPCNA subunit. This structural versatility of PCNA may be involved in the mechanisms for ring opening and closing.

Keywords: DNA replication; sliding clamp; X-ray diffraction; Archaea; hyperthermophile

	Introduction

TOP Abstract Introduction Results Discussion Materials and methods References

 
DNA replication and repair processes play central roles for the sustenance of life. Extensive studies on the molecular mechanism of DNA replication revealed the existence of a molecule that retains DNA polymerase on the template DNA strand for processive DNA synthesis (reviewed in Waga and Stillman 1998; Hingorani and O’Donnell 2000; Bruck and O’Donnell 2001; Trakselis and Benkovic 2001). This processivity factor of the DNA polymerases forms a dimer or trimer depending on the organism’s domain of life. The bacterial DNA polymerase III ß subunit exists as dimer, whereas the proliferating cell nuclear antigens (PCNA) from eukarya and archaea form homotrimers. The gp43 protein from bacteriophages also forms a homotrimeric structure. These proteins, often called sliding clamps, capture dsDNA within the central hole of the ring shaped dimer or trimer and directly interact with the replicative DNA polymerases. The eukaryotic PCNA also anchors various proteins involved in DNA repair, cell cycle control, and apoptotic processes (reviewed in Jonsson and Hubscher 1997; Kelman 1997; Kelman and Hurwitz 1998; Tsurimoto 1998, 1999; Warbrick 1998, Warbrick 2000; Paunesku et al. 2001). From these studies, it is now well recognized that the molecular analyses of PCNA are very important to elucidate the structure–function relationships of this multifunctional molecule.

The proteins related to the genetic information system in Archaea, the third domain of life, are structurally more similar to eukaryotic proteins than to those from Bacteria (reviewed for DNA replication in Edgell and Doolittle 1997; Ishino and Cann 1998; Cann and Ishino 1999; Leipe et al. 1999). We cloned a gene encoding a sequence homologous to the eukaryotic PCNA from the hyperthermophilic euryarchaeote, Pyrococcus furiosus, expressed it in Escherichia coli, and characterized the purified gene product (Cann et al. 1999). The protein interacted with both DNA polymerases I (Pol BI) and II (Pol D) in this organism and enhanced their DNA synthesizing activities in vitro, and therefore, we designated it as PfuPCNA. We have also determined the crystal structure of PfuPCNA and compared it with those of the human and yeast PCNAs (Matsumiya et al. 2001).

The three dimensional structures of the DNA sliding clamps have been determined for eukaryotes (Krishna et al. 1994; Gulbis et al. 1996), bacteriophages (Shamoo and Steitz 1999; Moarefi et al. 2000), and a bacterium (Kong et al. 1992) to date, in addition to the archaeal PCNA. All of these structures share the toroidal morphology with a pseudo-sixfold symmetry, and the archaeal and eukaryotic PCNAs are especially similar among them. The structural similarity of the PCNAs in Archaea and Eukarya is supported by the experiments showing that PfuPCNA functionally interacts with calf thymus DNA polymerase and human replication factor C (RFC) in vitro (Ishino et al. 2001). The Thermococcus PCNA also stimulates the calf thymus DNA polymerase activity (Henneke et al. 2000).

Although the overall structure of PfuPCNA resembles those of the human and yeast PCNAs, the mode of the intermolecular interactions between neighboring molecules differs between the archaeal and eukaryotic PCNAs. In the PfuPCNA trimer, the number of intermolecular main chain hydrogen bonds is lower, and the side chains of acidic and basic amino acids form an intermolecular ion pair network. We previously proposed that the formation of the ion pair network at the boundary between the subunits compensates for the weakening of the hydrogen bonds, to maintain the trimeric structure of PfuPCNA (Matsumiya et al. 2001). In this article, we report the biochemical properties of two mutant PfuPCNAs, in which one and two aspartates at the intermolecular interface are replaced with alanines, and examine the effects of the mutations on the molecular structures.

	Results

TOP Abstract Introduction Results Discussion Materials and methods References

 
Mutations of Asp143 to Ala and Asp147 to Ala in PfuPCNA
On the basis of the crystal structure of PfuPCNA (Matsumiya et al. 2001), the residues participating in the formation of the intermolecular ion pair network are distributed on each side of the intermolecular interfaces. Positively charged residues in the N-terminal domain (Arg82, Lys84, and Arg109) and negatively charged residues in the C-terminal domain (Glu139, Asp143, and Asp147) are participated in the ion pair network of the intermolecular interfaces of the PCNA ring structure. We substituted Asp143 and Asp147 with Ala to investigate the roles of the ion pair network in the interaction between the subunits. The plasmid pTPCNAL73 (Matsumiya et al., 2001) was used as a template and a PCR-mediated site-specific mutagenesis was performed. Two rounds of PCR were performed to introduce the two mutations into the gene, corresponding to Asp143Ala and Asp147Ala. The overexpression and purification procedures for the wild-type PfuPCNA were applied to obtain the desired mutant PCNAs, PfuPCNA (D143A) and PfuPCNA(D143A/D147A). These mutant PCNA proteins displayed the same profiles as those of the wild-type PfuPCNA in the ion-exchange chromatography, and were purified to homogeneity (Fig. 1).

View larger version (14K): [in this window] [in a new window]   Figure 1. Purification of mutant PfuPCNA proteins. Recombinant PfuPCNA proteins purified as described in the text were loaded onto a 12.5% polyacrylamide gel electrophoresis and stained with Coomassie brilliant blue. Molecular masses indicated on the left side were from the marker proteins (New England Biolabs).

View larger version (15K): [in this window] [in a new window]   Figure 2. Investigation of trimer formation by gel filtration analysis. The wild-type and mutant PfuPCNA proteins were subjected to a gel filtration column. Elution of the proteins was monitored by absorbance at 280 nm. The molecular masses on the top were from a gel filtration standard (BioRad), containing thyroglobulin (670 kD), -globulin (158 kD), ovalbumin (44 kD), myoglobulin (17 kD).

For the eukaryotic PCNA and the bacterial Pol III ß subunit, trimer or dimer formation is essential for their activities as processivity factors for DNA polymerases. We examined the stimulation activity of mutant PfuPCNAs on the DNA synthesis reaction by P. furiosus Pol I in the presence or absence of the PfuRFC complex to determine the effect of the mutation on the function as the sliding clamp under both RFC-assisted and self-loading conditions. As shown in Figure 3, PfuPCNA(D143A/D147A) did not show any stimulation of DNA synthesis by Pol I, in either the presence or absence of PfuRFC (lanes 4 and 7). In contrast, the wild-type and PfuPCNA(D143A) proteins enhanced the processivity of Pol I in both the presence and absence of PfuRFC (lanes 2, 3, 5, and 6). It is noteworthy that PfuPCNA(D143A) stimulated the Pol I reaction more extensively than the wild-type PfuPCNA, especially under the RFC-free condition. These results indicate that PfuPCNA (D143A) can form the active ring structure in solution, although the monomeric form is dominant in the gel filtration. The stronger activity of PfuPCNA (D143A) may be caused by the weaker intermolecular ion pair interaction, which made the trimeric ring much easier to open and close for loading onto and unloading from the DNA strand.

View larger version (65K): [in this window] [in a new window]   Figure 3. Effects of the mutations in PfuPCNA on the DNA synthesis reaction by P. furiosus Pol I. The reaction mixtures with indicated PfuPCNA proteins in each lane, both in the presence and absence of PfuRFC, were analyzed by 1% alkali agarose gel electrophoresis, and the products were visualized by autoradiography. The sizes indicated on the left were from BstI-digested phage DNA labeled by 32P at each 5' end.

View larger version (28K): [in this window] [in a new window]   Figure 4. Subunit interactions in the three PfuPCNA crystals and comparison of interdomain angles. Wild-type PfuPCNA forms a troidal trimer with C-terminal domain to N-terminal domain alignment (two molecules in the trimer are shown here). Both two mutant PfuPCNAs form V-shaped dimers with C-terminal to C-terminal alignment. Interdomain angles at the intramolecular interface and the intermolecular interface were represented by 1 and 2, respectively.

View larger version (60K): [in this window] [in a new window]   Figure 5. Hydrogen bonds at the intermolecular interfaces in the three PfuPCNA crystals. Hydrogen bonds (N...O 3.3 Å) observed in the trimer (wild-type) or dimer (mutants) of PfuPCNAs between the subunits are shown as red dashed lines.

The C-terminal domain of the wild-type PfuPCNA swings counterclockwise in the complex with the RFCL PIP-box peptide, compared with that in the uncomplexed form. Along with the swing motion, the interdomain torsion angle decreases from 59.7° in the uncomplexed form to 52.7° in the complexed form (Matsumiya et al. 2002). A similar motion is also predicted in the human PCNA–p21^WAF1/CIP1 C-terminal complex (Gulbis et al. 1996), by comparing the crystal structure with that of the uncomplexed form of yeast PCNA (Krishna et al. 1994) from 59.1° in yeast PCNA to 53.7°–54.4° in the human PCNA-p21 complex. In the crystals of the mutant PfuPCNAs (dimer form), in which the N-terminal domain is not fixed, the interdomain torsion angles are lower than that of the uncomplexed wild-type PfuPCNA (trimer form; Fig. 6): they are 55.1° for PfuPCNA (D143A) and 51.8°–52.1° for PfuPCNA(D143A/D147A). In the case of the Pol III ß subunit of E. coli, the difference in the interdomain dihedral angles in the closed ring dimer and the monomeric mutant is not remarkable. The only difference is at the interface between the N-terminal domain and the center domain of chain A of the ß subunit–full-length subunit complex (62.7°–64.6° in wild type to 57.1° in the complex), but this decrease in the dihedral angle is probably compensated by the increase in the center domain–C-terminal domain interface by subunit binding. Because in the ß– (1–140) complex, the center domain–C-terminal domain torsion angle (54.9°) is smaller than that of the wild type, the increase in the ß– (full-length) complex may reflect the flexibility at the interdomain interfaces.

View larger version (37K): [in this window] [in a new window]   Figure 6. Domain movement in the mutant PfuPCNA crystals. The monomer structures of the two mutant PfuPCNA crystals were superimposed on the wild-type structure. The wild-type, D143A, and D143A/D147A are indicated in blue, green, and red, respectively. A side view (left) and a top view (right) are shown. In the side view, the N-terminal and the C-terminal domains are shown with a thin and a thick line, respectively.

	Discussion

TOP Abstract Introduction Results Discussion Materials and methods References

The structural differences of the wild-type PfuPCNA (Matsumiya et al. 2001), its complex with the PIP-box peptide from the large subunit (RFCL) of PfuRFC (Matsumiya et al. 2002), and the mutant PfuPCNA in this study induced by crystal packing force revealed the conformational flexibility of the interdomain or intermolecular interface of the PCNA molecules. This conformational versatility of PfuPCNA may contribute to the functional change of the ring structure. A comparison of the interdomain angles between the dimeric wild-type and the monomeric mutant of the E. coli Pol III ß subunit support the in-plane open ring model (Jeruzalmi et al. 2001). The proposed model for the ß subunit includes an expansion at the interface between the N-terminal and center domains, although the subunit, the "wrench" of the clamp loader binds on the interface between the central and C-terminal domains (Jeruzalmi et al. 2001). The dynamic structural model for the replisome in bacteriophage T4, gp45 (clamp)–gp44/62 (clamp loader)– gp43 (DNA polymerase), has recently been determined using a stopped-flow fluorescence energy transfer technique (Alley et al. 2000; Trakselis et al. 2001). The proposed model for the opening and closing of the gp45 clamp includes an in-plane opening at the initial stage, an out-of-plane, partially closed conformation upon DNA capture, and an in-plane, slightly open final form complexed with gp43 (Trakselis et al. 2001).

The interdomain angles of the mutant PfuPCNAs were similar to or narrower than those of the wild-type PfuPCNA, in contrast to the case of the mutant E. coli Pol III ß subunit. It does not appear that this structural difference supports the in-plane mode for the ring opening of PfuPCNA. Based on the monomeric structure of mutant PfuPCNAs, a hypothetical trimer was built (Fig. 7). The ring is opened with an out-of-plane distortion in this model. The structural differences between the PfuPCNA and PfuPCNA–PIP box peptide, and also between yeast PCNA and the human PCNA–p21 peptide complex (Matsumiya et al. 2002) support the idea that the out-of-plane movement, derived from the conformational flexibility between the domains, may be in common in the archaeal and eukaryotic PCNA.

View larger version (30K): [in this window] [in a new window]   Figure 7. An open ring model of PfuPCNA trimer based on structural comparisons between wild-type and mutant PfuPCNA crystals. A ring structure model was built by superposing the monomer structure of D143A/D147A on the intermolecular interfaces of the wild-type structure. Two orthogonal views (a top view, left, and a side view, right) are shown. Three subunits are indicated by different colors.

	Materials and methods

TOP Abstract Introduction Results Discussion Materials and methods References

 
Preparation of mutant PfuPCNA proteins
The plasmid pTPCNAL73 (Matsumiya et al. 2001), in which the gene for PfuPCNA (Met73Leu) is inserted into the pET21a vector (Novagen), was used for the polymerase chain reaction (PCR)-mediated mutagenesis. Because no difference was observed between wild-type and M73L mutant PCNA in our biologic analyses (Matsumiya et al. 2001), PfuPCNA(M73L) is called "wild-type PfuPCNA" in this study. In the first stage, two primers, PCNA MUTF2 (5'-TTCTTGGAGAAGTCCTAAAAGCTGCTGTTAA AGATGCCTCTCTAGTGAGTGACAG-3') and PCNAMUTR2 (5'-CTGTCACTCACTAGAGAGGCATCTTTAACAGCAGCTTTTAGGACTTCTCCAAGAA-3'), which have the codons corresponding to alanine instead of aspartate at position 143 (underlined), were used for the PCR reaction. The PCR conditions involved 30 cycles of denaturation for 30 sec at 95°C, annealing for 1 min at 55°C, and extension for 10 min at 68°C with Pyrobest DNA polymerase (Takara Shuzo). The amplified product was treated with DpnI for 1 h at 37°C and was introduced into E. coli JM109 cells. The plasmids isolated from the transformants were sequenced, and the plasmid encoding the Asp143Ala mutant was selected. The mutant plasmid was designated as pTPCNAA143. In the second stage, the same procedure was adopted with pTPCNAA143 as the template and the primers PCNAMUTF1 (5'-TTCTTGGAGAAGTCCTAAAAGCTGCTGTTAAAGCTGCCTCTCTAGTGAGTGACAG-3') and PCNAMUTR1 (5'-CTGTCACTCACTAGAGAGGCAGCTTTAACAGCAGCTTTTAGGACTTCTCCAAGAA-3'), which contain two alanine codons instead of aspartates at positions 143 and 147 (underlined) as the primers. The resultant plasmid was designated as pTPCNAA147. The mutant PfuPCNAs, PfuPCNA(D143A) and PfuPCNA(D143A/D147A), were overproduced in E. coli BL21(DE3) cells and were purified according to the protocol described for the wild-type PfuPCNA (Cann et al. 1999). The purified mutant PfuPCNA solutions were concentrated to 20 mg/mL by ultrafiltration and were stored at 4°C.

Gel filtration analysis
Solutions (1.0 mg/mL; 36 µM) of the mutant PfuPCNAs were subjected to gel filtration on a Superdex 200 PC 3.2/30 column (Amersham Pharmacia Biotech) in a 50 mM Tris-HCl, pH 8.0, 150 mM NaCl solution. The molecular weights of the solutes were estimated from the retention volume, using those of the Gel Filtration Standards (Bio-Rad) as the standards.

Assay of primer extension stimulation
The effects of the mutant PfuPCNAs on the DNA synthesis activity were assayed by using P. furiosus Pol I (Komori and Ishino 2000) and M13 single-stranded DNA annealed with a deoxyoligonucleotide primer, as described previously, in the presence or absence of the PfuRFC complex (Cann et al. 1999, 2001).

Crystallization and data collection
Single crystals of the mutant PfuPCNAs were prepared by the hanging drop vapor diffusion method. A 1.0 µL aliquot of the protein solution and 1.0 µL of precipitation buffer were mixed and equilibrated against 500 µL of precipitation buffer at 20°C. The compositions of the precipitation buffers were as follows: 100 mM sodium citrate pH 4.5, 0.6 M ammonium sulfate and 40% (v/v) glycerol for PfuPCNA(D143A), and 100 mM sodium citrate pH 5.5, 2.6 M ammonium sulfate, 11% (v/v) 2-methyl-2,4-pentanediol and 4% (v/v) glycerol for PfuPCNA(D143A/D147A). The colorless octahedrons of PfuPCNA(D143A) or colorless plates of PfuPCNA(D143A/D147A) were obtained in a week. The crystals could be flash-cooled without cryoprotection. X-ray diffraction data were collected at 100 K on the BL24XU beamline of SPring-8 using 0.836 Å radiation and an R-AXIS V imaging plate detector (Rigaku Corporation). The data were processed by MOSFLM (Leslie 1992), scaled, and converted for crystal structure determination with SCALA and TRUNCATE in the CCP4 program suite (Collaborative Computational Project, Number 4, 1994).

Structure determination
The crystal structures of the mutant PfuPCNAs were determined by the molecular replacement method using CNS (Brünger et al. 1998), with the structure of PfuPCNA (Matsumiya et al., 2001; PDB code 1GE8) as the search model. In the case of PfuPCNA(D143A), the solution with the highest correlation factor after the rotation and translation search yielded a reasonable model for the structure refinement. In the case of PfuPCNA(D143A/D147A), the two molecules in the asymmetric unit were placed by two cycles of the translation search after the rotation search. Because the two molecules formed a dimer around an apparent twofold axis, a noncrystallographic symmetry (NCS) restraint was applied in the structure refinement stage. The molecular structures were manually built using O (Jones et al. 1991), and were refined by the simulated annealing method using CNS. The residues Met1, Met121–Leu125, and Glu248–Glu249 could not be modeled because of the poor electron densities at these regions. The results of the crystal structure analyses are summarized in Table 1. The molecular coordinates and structure factors have been deposited in the Protein Data Bank under the ID codes 1IZ4 (for D143A) and 1IZ5 (for D143A/D147A).

	Acknowledgments

 
We thank Y. Katsuya for help with the use of the SPring-8 BL24XU beamline. This work was supported in part by New Energy and Industrial Technology Development Organization (NEDO) in the Japanese Government.

	References

TOP Abstract Introduction Results Discussion Materials and methods References

 
Alley, S.C., Abel-Santos, E., and Benkovic, S.J. 2000. Tracking sliding clamp opening and closing during bacteriophage T4 DNA polymerase holoenzyme assembly. Biochemistry 39: 3076–3090.[CrossRef][Medline]

Ayyagari, R., Impellizzeri, K.J., Yoder, B.L., Gary, S.L., and Burgers, P.M. 1995. A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair. Mol. Cell. Biol. 15: 4420–4429.[Abstract]

Bruck, I. and O’Donnell, M. 2001. The ring-type polymerase sliding clamp family. Genome Biol. 2: 3001.1–3001.3.

Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J-S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D54: 905–921.

Cann, I.K.O. and Ishino, Y. 1999. Archaeal DNA replication: Identifying the pieces to solve a puzzle. Genetics 152: 1249–1267.[Abstract/Free Full Text]

Cann, I.K.O., Ishino, S., Hayashi, I., Komori, K., Toh, H., Morikawa, K., and Ishino, Y. 1999. Functional interactions of a homolog of proliferating cell nuclear antigen with DNA Polymerases in Archaea. J. Bacteriol. 181: 6591–6599.[Abstract/Free Full Text]

Cann, I., Ishino, S., Yuasa, M., Daiyasu, H., Toh, H., Morikawa, K., and Ishino, Y. 2001. Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 183: 2614–2623.[Abstract/Free Full Text]

Collaborative Computational Project, Number 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50: 760–763.

Edgell, D.R. and Doolittle, W.F. 1997. Archaea and the origin(s) of DNA replication proteins. Cell 89: 995–998.[CrossRef][Medline]

Ellison, V. and Stillman, B. 2001. Opening of the clamp: An intimate view of an ATP-driven biological machine. Cell 106: 655–660.[CrossRef][Medline]

Gulbis, J.M., Kelman, Z., Hurwitz, J., O’Donnell, M., and Kuriyan, J. 1996. Structure of the C-terminal region of p21^WAF1/CIP1 complexed with human PCNA. Cell 87: 297–306.[CrossRef][Medline]

Henneke, G., Raffin, J.P., Ferrari, E., Jonsson, Z.O., Dietrich, J., and Hubscher, U. 2000. The PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase . Biochem. Biophys. Res. Commun. 276: 600–606.[CrossRef][Medline]

Hingorani, M.M. and O’Donnell, M. 2000. Sliding clamps: A tailored fit. Curr. Biol. 10: R25–R29.[CrossRef][Medline]

Ishino, Y. and Cann, I.K.O. 1998. The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: Fact or farce? Genes Genet. Syst. 73: 323–336.[CrossRef][Medline]

Ishino, Y., Tsurimoto, T., Ishino, S., and Cann, I.K.O. 2001. Functional interactions of an archaeal sliding clamp with mammalian clamp loader and DNA polymerase . Genes Cells 6: 699–706.[Abstract]

Jeruzalmi, D., Yurieva, O., Zhao, Y., Young, M., Stewart, J., Hingorani, M., O’Donnell, M., and Kuriyan, J. 2001. Mechanism of processivity clamp opening by the subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 106: 417–428.[CrossRef][Medline]

Jeruzalmi, D., O’Donnell, M.M., and Kuriyan, J. 2002. Clamp loaders and sliding clamps. Curr. Opin. Struct. Biol. 12: 217–224.[CrossRef][Medline]

Jones, T.A., Zou, J-Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47: 110–119.

Jonsson, Z.O. and Hubscher, U. 1997. Proliferating cell nuclear antigen: More than a clamp for DNA polymerase. Bioessays 19: 967–975.[CrossRef][Medline]

Jonsson, Z.O., Podust, V.N., Podust, L.M., and Hubscher, U. 1995. Tyrosine 114 is essential for the trimeric structure and the functional activities of human proliferating cell nuclear antigen. EMBO J. 14: 5745–5751.[Medline]

Kelman, Z. 1997. PCNA: Structure, functions, and interactions. Oncogene 14: 629–640.[CrossRef][Medline]

Kelman, Z. and Hurwitz, J. 1998. Protein–PCNA interactions: A DNA-scanning mechanism? Trends Biochem. Sci. 23: 236–238.[CrossRef][Medline]

Komori, K. and Ishino, Y. 2000. Functional interdependence of DNA polymerizing and 3' 5' exonucleolytic activities in Pyrococcus furiosus DNA polymerase I. Protein Eng. 13: 41–47.[Abstract/Free Full Text]

Kong, X.P., Onrust, R., O’Donnell, M., and Kuriyan, J. 1992. Three dimensional structure of the ß subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp. Cell 69: 425–437.[CrossRef][Medline]

Krishna, T.S.R., Kong, X.P., Gary, S., Burgers, P.M., and Kuriyan, J. 1994. Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233–1243.[CrossRef][Medline]

Leipe, D.D., Aravind, L., and Koonin, E.V. 1999. Did DNA replication evolve twice independently? Nucleic Acids Res. 27: 3389–3401.[Abstract/Free Full Text]

Leslie, A.G.W. 1992. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography, No. 26.

Matsumiya, S., Ishino, Y., and Morikawa, K. 2001. Crystal structure of an archaeal DNA sliding clamp: Proliferating cell nuclear antigen from Pyrococcus furiosus. Protein Sci. 10: 17–23.[Abstract/Free Full Text]

Matsumiya, S., Ishino, S., Ishino, Y., and Morikawa, K. 2002. Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus. Genes Cells 7: 911–922.[Abstract]

McAlear, M.A., Howell, E.A., Espenshade, K.K., and Holm, C. 1994. Proliferating cell nuclear antigen (pol30) mutations suppress cdc44 mutations and identify potential regions of interaction between the two encoded proteins. Mol. Cell. Biol. 14: 4390–4397.[Abstract/Free Full Text]

Moarefi, I., Jeruzalmi, D., Turner, J., O’Donnell, M., and Kuriyan, J. 2000. Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. J. Mol. Biol. 296: 1215–1223.[CrossRef][Medline]

O’Donnell, M., Jeruzalmi, D., and Kuriyan, J. 2001. Clamp loader structure predicts the architecture of DNA polymerase III holoenzyme and RFC. Curr. Biol. 11: R935–R946.[CrossRef][Medline]

Oyama, T., Ishino, Y., Cann, I.K.O., Ishino, S. and Morikawa, K. 2001. Atomic structure of the clamp loader small subunit from Pyrococcus furiosus. Mol. Cell 8: 455–463.[CrossRef][Medline]

Paunesku, T., Mittal, S., Protic, M., Oryhon, J., Korolev, S.V., Joachimiak, A., and Woloschak, G.E. 2001. Proliferating cell nuclear antigen (PCNA): Ringmaster of the genome. Int. J. Radiat. Biol. 77: 1007–1021.[CrossRef][Medline]

Shamoo, Y. and Steitz, T.A. 1999. Building a replisome from interacting pieces: Sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 99: 155–166.[CrossRef][Medline]

Stewart, J., Hingorani, M.M., Kelman, Z., and O’Donnell, M. 2001. Mechanism of ß clamp opening by the subunit of Escherichia coli DNA polymerase III holoenzyme. J. Biol. Chem. 276: 19182–19189.[Abstract/Free Full Text]

Trakselis, M.A. and Benkovic, S. J. 2001. Intricacies in ATP-dependent clamp loading: Variations across replication systems. Structure 9: 999–1004.[Medline]

Trakselis, M.A., Alley, S.C., Abel-Santos, E., and Benkovic, S.C. 2001. Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. 98: 8368–8375.[Abstract/Free Full Text]

Tsurimoto, T. 1998. PCNA, a multifunctional ring on DNA. Biochim. Biophys. Acta 1443: 23–39.[Medline]

———. 1999. PCNA binding proteins. Front. Biosci. 4: 849–858.

Waga, S. and Stillman, B. 1998. The DNA replication fork in eukaryotic cells. Annu. Rev. Biochem. 67: 721–751.[CrossRef][Medline]

Warbrick, E. 1998. PCNA binding through a conserved motif. BioEssays 20: 195–199.[CrossRef][Medline]

———. 2000. The puzzle of PCNA’s many partners. BioEssays 22: 997–1006.[CrossRef][Medline]

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