PDBsum entry 2io4

DNA binding protein

PDB id: 2io4

Contents

Protein chains

249 a.a. *

246 a.a. *

Ligands

MPD ×5

Metals

_CA

Waters ×171

* Residue conservation analysis

PDB id:

2io4

Name:

DNA binding protein

Title:

Crystal structure of pcna12 dimer from sulfolobus solfataricus.

Structure:

DNA polymerase sliding clamp b. Chain: a, c. Synonym: proliferating cell nuclear antigen homolog b, pcna b. Engineered: yes. Mutation: yes. DNA polymerase sliding clamp c. Chain: b, d. Synonym: proliferating cell nuclear antigen homolog c, pcna c. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 273057. Strain: p2. Gene: pcnb, pcna-2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: pcnc, pcna-2.

Resolution:

2.60Å R-factor: 0.234 R-free: 0.260

Authors:

V.Hlinkova,H.Ling

Key ref:

V.Hlinkova et al. (2008). Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening. Acta Crystallogr D Biol Crystallogr, 64, 941-949. PubMed id: 18703842 DOI: 10.1107/S0907444908021665

Date:

09-Oct-06 Release date: 08-Apr-08

Protein chains

P57766  (PCNA1_SULSO) -  DNA polymerase sliding clamp 1 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 249 a.a.

Struc: 249 a.a.*

Protein chains

Q97Z84  (PCNA2_SULSO) -  DNA polymerase sliding clamp 2 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 245 a.a.

Struc: 246 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.?

DOI no: 10.1107/S0907444908021665

Acta Crystallogr D Biol Crystallogr 64:941-949 (2008)

PubMed id: 18703842

Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.

V.Hlinkova, G.Xing, J.Bauer, Y.J.Shin, I.Dionne, K.R.Rajashankar, S.D.Bell, H.Ling.

ABSTRACT

DNA sliding clamps form an oligomeric ring encircling DNA and serve as a moving platform for DNA-processing proteins. The opening and closing of a sliding-clamp ring is essential to load the clamp onto DNA in order to perform its functions. The molecular details of how clamp rings open and enclose DNA are still not clear. Three PCNA homologues have been found in Sulfolobus solfataricus which form a heterotrimer. Taking advantage of their hetero-oligomeric nature, the structures of the PCNAs in monomeric PCNA3, dimeric PCNA1-PCNA2 and trimeric PCNA1-PCNA2-PCNA3 forms were determined at resolutions of 2.6-1.9 A. The distinct oligomeric structures represent different stages in ring formation, which were verified in solution by ultracentrifugation analysis. The heterodimer opens in a V-shape of 130 degrees , while the heterotrimers form a ring with a 120 degrees rotation between monomers. The association of a rigid PCNA3 monomer with an opened PCNA1-PCNA2 heterodimer closes the ring and introduces a spring tension in the PCNA1-PCNA2 interface, thus bending the nine-stranded intermolecular beta-sheet to fit the 120 degrees rotation. The release of the spring tension as PCNA3 dissociates from the ring may facilitate ring opening. The structural features in different assemblies present a molecular model for clamp ring assembly and opening.

Selected figure(s)

Figure 4.
Figure 4 The three distinct ligand-binding sites of the PCNA123 trimer. The front face of the trimeric ring is shown as an electrostatic charged surface with the C-terminal fragment of Pol IV modeled in the three distinct ligand-binding sites. The binding sites are mapped by ribbon-styled C-termini with the side chains as white mesh surfaces. The modeling was performed by superposing the PCNA123 trimer with the -clamp-PolIV-LF complex (PDB code 1ok7 ; Bunting et al., 2003[Bunting, K. A., Roe, S. M. & Pearl, L. H. (2003). EMBO J. 22, 5883-5892.]).

Figure 7.
Figure 7 Assembly and opening of the PCNA123 ring. (a) PCNA12 dimer and PCNA3 monomer approaching each other during ring assembly. (b) The ring of the PCNA123 trimer. (c) PCNA12 dimer with PCNA3 modeled in contact with PCNA2 with an angle of 120° as in the trimer. A gap (6-7 Å) remains in the ring-shaped molecule as the angle between PCNA1 and PCNA2 is 130° instead of 120°.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 941-949) copyright 2008.

Figures were selected by an automated process.