PDBsum entry 1iqp

Replication

PDB id

1iqp

Contents

			Protein chains

					(+ 0 more) 326 a.a. *

			Ligands

					ADP ×4

			Waters ×244

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Atomic structure of the clamp loader small subunit from pyrococcus furiosus.

Authors

T.Oyama, Y.Ishino, I.K.Cann, S.Ishino, K.Morikawa.

Ref.

Mol Cell, 2001, 8, 455-463. [DOI no: 10.1016/S1097-2765(01)00328-8]

PubMed id

11545747

Abstract

In eukaryotic DNA replication, replication factor-C (RFC) acts as the clamp loader, which correctly installs the sliding clamp onto DNA strands at replication forks. The eukaryotic RFC is a complex consisting of one large and four small subunits. We have determined the crystal structure of the clamp loader small subunit (RFCS) from Pyrococcus furiosus. The six subunits, of which four bind ADP in their canonical nucleotide binding clefts, assemble into a dimer of semicircular trimers. The crescent-like architecture of each subunit formed by the three domains resembles that of the delta' subunit of the E. coli clamp loader. The trimeric architecture of archaeal RFCS, with its mobile N-terminal domains, involves intersubunit interactions that may be conserved in eukaryotic functional complexes.



	Figure 1. Figure 1. Crystal Structure of P. furiosus RFCS(A) The overall fold of an RFCS subunit is shown by a ribbon representation. α helices and β strands are drawn by coils and arrows, respectively. The chain is colored cyan for Domain 1, green for Domain 2, and yellow for Domain 3. Walker A and B motifs are colored red. ADP is shown as a purple stick model.(B) The RFCS hexamer in the crystal is shown as a ribbon diagram viewed from the N-terminal side. The six subunits are colored blue, magenta, cyan, green, orange, and yellow-green for MolA to MolF, respectively. The four ADP molecules bound to MolA, MolB, MolC, and MolE are shown as red stick models.(C) A stereo view of an omit F[o]-F[c] electron density map contoured at 3 σ (ρ), drawn with ADP. Amino acid residues interacting with ADP are depicted. Water molecules are indicated by white spheres.(D) Orthogonal views of electrostatic potential mapped onto the molecular surfaces as calculated by the program GRASP (Nicholls and Honig, 1991). Positively charged surfaces are colored blue, and negatively charged surfaces are red. The figure in the upper left panel is viewed from the N-terminal side, as in (B). Trimer 1 (MolA to MolC) is indicated by a dotted line in the upper left (N-terminal side) and upper right (C-terminal side) panels		Figure 3. Figure 3. Structure of RFCS Hexamers(A) Comparison of a hypothetical hexameric ring of RFCS (center) with the electron microscopic image (left). The 6-fold symmetry ring model was built from a semicircular trimer of RFCS in the crystal (right) and is drawn in top (upper) and side views (lower). One subunit in each hexamer is encircled. The EM 3D reconstructed images were obtained by essentially the same procedure as in our previous study (Mayanagi et al., 2001; K. Mayanagi and T. Miyata, personal communication). The scale bar indicated for the EM images is 50 Å.(B) Interaction scheme between subunits within the semicircular trimers, represented by an open-book view. Subunits with interfaces near the convex side of the crescent-shaped molecules are designated as “front,” while those with interfaces at the inner concave region of the crescents are designated as “back.” Only MolA and MolB are drawn as representative subunits. Segments contributing to the interfaces are colored blue for the front subunit and magenta for the back. In the front subunit, four segments, residues 4–14, 206–210, 229–231, and 262–271, contribute to Interface I (upper half), while two segments, residues 249–255 and 300–323, form Interface II (lower half). In the back subunit, residues 36–47 and 149–168 are involved in Interface I and residues 277–309 in Interface II. Intersubunit hydrogen bonding and hydrophobic interactions, which are observed in more than two interfaces of the total four, are indicated by red and green lines, respectively