PDBsum entry 1u98

DNA binding protein

PDB id

1u98

Contents

			Protein chain

					311 a.a. *

			Ligands

					SO4


					GOL ×2

			Waters ×172

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structures of escherichia coli reca in a compressed helical filament.

Authors

X.Xing, C.E.Bell.

Ref.

J Mol Biol, 2004, 342, 1471-1485. [DOI no: 10.1016/j.jmb.2004.07.091]

PubMed id

15364575

Abstract

The X-ray crystal structure of uncomplexed Escherichia coli RecA protein has been determined in three new crystal forms at resolutions of 1.9 A, 2.0 A, and 2.6 A. The RecA protein used for this study contains the extra residues Gly-Ser-His-Met at the N terminus, but retains normal ssDNA-dependent ATPase and coprotease activities. In all three crystals, RecA is packed in a right-handed helical filament with a pitch of approximately 74 A. These RecA filaments are compressed relative to the original crystal structure of RecA, which has a helical pitch of 82.7 A. In the structures of the compressed RecA filament, the monomer-monomer interface and the core domain are essentially the same as in the RecA structure with the 83 A pitch. The change in helical pitch is accommodated by a small movement of the N-terminal domain, which is reoriented to preserve the contacts it makes at the monomer-monomer interface. The new crystal structures show significant variation in the orientation and conformation of the C-terminal domain, as well as in the inter-filament packing interactions. In crystal form 2, a calcium ion is bound closely to a beta-hairpin of the C-terminal domain and to Asp38 of a neighboring filament, and residues 329-331 of the C-terminal tail become ordered to contact a neighboring filament. In crystal forms 3 and 4, a sulfate ion or a phosphate anion is bound to the same site on RecA as the beta-phosphate group of ADP, causing an opening of the P-loop. Altogether, the structures show the conformational variability of RecA protein in the crystalline state, providing insight into many aspects of RecA function.



	Figure 1. Figure 1. Structure of the RecA monomer from the form 2 crystal. The orientation is the same as for the uppermost monomer (magenta) from the form 2 filament shown in Figure 2c. The a-helices and b-strands of RecA are labeled according to form 1.12 The three calcium ions on the surface are shown as magenta spheres. Residues 66-71 of the P-loop of the ATP-binding site are colored green. Residues 329-331 of the C-terminal tail, which are ordered only in form 2, are shown in blue bonds. The last ordered residues at the ends of loops L1 and L2 are highlighted in orange and red, respectively.		Figure 5. Figure 5. The N-terminal domain rotates to accommodate compression of the RecA filament. a, Two neighboring monomers in the RecA filament are shown in yellow and cyan in an orientation similar to that of the subunits on the front of the filaments shown in Figure 2. This orientation is chosen to optimize the visibility of the monomer-monomer interaction. Form 1 (PDB code 2REB)12 is shown in continuous lines and form 2 is shown in broken lines. The form 1 and 2 structures are superimposed on the basis of the C^a atoms of the core domains of the monomer on the left. The difference in the helical transformation in forms 1 and 2 is evident from the poor overlap of the monomer on the right. Residues 6 and 33 are labeled to indicate the boundaries of the N-terminal domain. b, Close-up view of a in the region of the monomer-monomer interface. Notice that the orientation of the N-terminal domain of the left monomer is different in the form 1 and form 2 structures, according to the position of the neighboring subunit. The orientation of the N-terminal domain is adjusted to accommodate changes in helical pitch, while preserving atomic interactions at the monomer-monomer interface. This is observed also in the form 3 and form 4 structures, though shown here only for the form 1 and form 2 structures.

PROCHECK

	Headers