PDBsum entry 2v1u

Replication

PDB id: 2v1u

Contents

Protein chain

382 a.a.

DNA/RNA

Ligands

ADP

Metals

_MG

Waters ×8

References listed in PDB file

Key reference

Title

Structural basis of DNA replication origin recognition by an orc protein.

Authors

M.Gaudier, B.S.Schuwirth, S.L.Westcott, D.B.Wigley.

Ref.

Science, 2007, 317, 1213-1216. [DOI no: 10.1126/science.1143664]

PubMed id

17761880

Abstract

DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additional DNA contacts are made with the N-terminal AAA+ domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35 degrees bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.

Figure 1.
Fig. 1. (A) Organization of the Ori1 replication origin in A. pernix. The four ORB sequences are located on either side of the DUE. The sequence of the 5'-to-3' ("top") strand of ORB4 is shown. (B) Overall structure of the ORC1-DNA complex. (C) Contacts between the AAA^+ domain and DNA. Thr^122 (T122) (21) contacts the Gd18-Cd5 base pair, L124 main chain oxygen contacts Gd19, and E128 contacts Gd20 via a water molecule. Residues T103, R106, G123, and R132 make direct interactions with the phosphodiester backbone on either side of the minor groove. (D) Insertion of the wing of the WH domain into the DNA minor groove widens it by 5 Å. Residues S366, G368, G371, and K372 interact directly with bases Td17, Gd18, and Gd19 of the complementary strand. G368, G371, K372, and T373 also interact with the DNA backbone on both sides of the minor groove. (E) Insertion of the recognition helix of the WH domain into the major groove. R345 makes a base-specific interaction with Gd10. Residues T343, R346, S348, and R374 contact the DNA phosphate backbone. The R346 side chain is stabilized in a noncanonical conformation by a salt bridge interaction with E353, which enables it to bind the DNA phosphate backbone. In the same way, interaction between S352 and R374 brings the arginine side chain close to the DNA backbone.

Figure 3.
Fig. 3. The stoichiometry of ORC1 binding at the ORB4 element. (A) Isothermal calorimetry data collected by using purified WH domain protein and a 40-mer DNA containing an ORB4 element. (B) Figure mapping the footprint data [(C)] onto the crystal structure. (C) Deoxyribonuclease I footprints across the ORB4 region. DNA sequences are indicated at the side for reference, with the ORB4 sequence boxed.

The above figures are reprinted by permission from the AAAs: Science (2007, 317, 1213-1216) copyright 2007.