PDBsum entry 1fnn

Cell cycle

PDB id: 1fnn

Contents

Protein chains

379 a.a.

Ligands

ADP ×2

Metals

_MG ×2

Waters ×327

References listed in PDB file

Key reference

Title

Structure and function of cdc6/cdc18: implications for origin recognition and checkpoint control.

Authors

J.Liu, C.L.Smith, D.Deryckere, K.Deangelis, G.S.Martin, J.M.Berger.

Ref.

Mol Cell, 2000, 6, 637-648. [DOI no: 10.1016/S1097-2765(00)00062-9]

PubMed id

11030343

Abstract

Cdc6/Cdc18 is a conserved and essential component of prereplication complexes. The 2.0 A crystal structure of an archaeal Cdc6 ortholog, in conjunction with a mutational analysis of the homologous Cdc18 protein from Schizosaccharomyces pombe, reveals novel aspects of Cdc6/Cdc18 function. Two domains of Cdc6 form an AAA+-type nucleotide binding fold that is observed bound to Mg.ADP. A third domain adopts a winged-helix fold similar to known DNA binding modules. Sequence comparisons show that the winged-helix domain is conserved in Orc1, and mutagenesis data demonstrate that this region of Cdc6/Cdc18 is required for function in vivo. Additional mutational analyses suggest that nucleotide binding and/or hydrolysis by Cdc6/Cdc18 is required not only for progression through S phase, but also for maintenance of checkpoint control during S phase.

Figure 4.
Figure 4. Nucleotide Binding by Cdc6A) Comparison of Cdc6 with various AAA^+ proteins. NSF-D2, Cdc6, and δ′ are shown in ribbon representation and colored cyan, green/red, and gold. Mg•ATP and Mg•ADP are shown bound to NSF-D2 and Cdc6, respectively, as black ball-and-stick. Structural comparisons between the AAA^+ regions of Cdc6, NSF-D2, and δ' can be made by using the core regions with sequence similarity as an additional guide: domain I of Cdc6 has an overall rmsd of 1.7 Å and 1.8 Å (spanning 100 and 79 residues) to NSF-D2, and δ′, respectively; domain II of Cdc6 superposes with the equivalent regions of NSF and δ' to 1.3 Å and 1.2 Å rmsd over 25 and 21 amino acids. Global rmsds spanning both domains are similar to individual domain rmsds for NSF-D2 and Cdc6 but are markedly different for cdc6 and δ′ (2.0 Å rmsd over 125 residues for NSF-D2 compared to 2.5 Å rmsd over 100 residues for δ′).(B) Stereogram view of the nucleotide binding region. Secondary structure is shown as a white coil. Residues within 4 Å of bound Mg•ADP are shown as gray ball-and-stick and are labeled; the one exception is His-167, which is part of the conserved sensor I motif but lies 5 Å away from the β-phosphate group. ADP is colored as magenta ball-and-stick, and the Mg^2+ ion and coordinating waters are shown as black and red spheres, respectively. Hydrogen bonds are shown as dashed lines. Backbone nitrogen atoms are shown as blue spheres and are exaggerated in size for emphasis.(A) and (B) generated by RIBBONS ([10]).

Figure 7.
Figure 7. Cdc6 Domain III(A) Ribbon diagram comparing the similar regions of Cdc6 domain III (right, gold) and histone H5 (left, blue). “HTH” and “W” designate the helix-turn-helix and wing regions, respectively. Secondary-structural elements of Cdc6 correspond to those in (C).(B) One model for domain III function. Domain III (gold) is shown docked onto duplex DNA (gray stick). To generate the model, domain III was superposed on E2F as seen in the E2F/DNA cocrystal structure ([63]). The rmsd between E2F and P. aerophilum Cdc6 domain III is 2.4 Å over 64 C[α] positions. Amino acids known to be important for appropriate Cdc6 activity are shown as magenta (null mutants) or cyan (2C-arrest mutants) ball-and-stick. It is interesting to note that, much like origin sequences, the surface of this domain is not conserved among Cdc6/Cdc18 orthologs. However, most of the observed mutations cluster on one side of the domain, and alleles 46 and 47 fall on or near the putative DNA binding elements (see Figure 6).(C) ClustalX ([59]) sequence alignment of the C-termini of Cdc6/Cdc18 and Orc1 orthologs. The secondary-structural elements observed in Cdc6 are drawn below as cylinders (α helices), arrows (β strands), and coil (lines). The P. aerophilum cdc6 and S. pombe cdc18^+ sequences are boxed in gray, while colors indicate regions of chemical conservation; for example, blue represents hydrophobic conservation, orange represents conservation of positively charged groups, etc.(A) and (B) generated by RIBBONS ([10]).

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 6, 637-648) copyright 2000.