PDBsum entry: 1xex

Cell cycle

PDB id: 1xex

Contents

Protein chains

166 a.a. *

161 a.a. *

Ligands

ATP

Metals

_MG

Waters ×129

* Residue conservation analysis

PDB id:

1xex

Name:

Cell cycle

Title:

Structural biochemistry of atp-driven dimerization and DNA stimulated activation of smc atpases.

Structure:

Smc protein. Chain: a. Fragment: smc_n-terminal fragment (residue 1-182). Engineered: yes. Smc protein. Chain: b. Fragment: smc_c-terminal fragment (residue 1006-1177). Engineered: yes. Mutation: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Gene: smc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.50Å R-factor: 0.207 R-free: 0.261

Authors:

A.Lammens,A.Schele,K.-P.Hopfner

Key ref:

A.Lammens et al. (2004). Structural biochemistry of ATP-driven dimerization and DNA-stimulated activation of SMC ATPases. Curr Biol, 14, 1778-1782. PubMed id: 15458651 DOI: 10.1016/j.cub.2004.09.044

Date:

13-Sep-04 Release date: 07-Dec-04

Protein chain

Q8TZY2  (SMC_PYRFU) -  Chromosome partition protein Smc

Seq: 1177 a.a.

Struc: 166 a.a.

Protein chain

No UniProt id for this chain

 Gene Ontology (GO) functional annotation 

• Cellular component: chromosome (1 term)
• Biochemical function: ATP binding (1 term)

DOI no: 10.1016/j.cub.2004.09.044

Curr Biol 14:1778-1782 (2004)

PubMed id: 15458651

Structural biochemistry of ATP-driven dimerization and DNA-stimulated activation of SMC ATPases.

A.Lammens, A.Schele, K.P.Hopfner.

ABSTRACT

Structural maintenance of chromosome (SMC) proteins play a central role in higher-order chromosome structure in all kingdoms of life. SMC proteins consist of a long coiled-coil domain that joins an ATP binding cassette (ABC) ATPase domain on one side and a dimerization domain on the other side. SMC proteins require ATP binding or hydrolysis to promote cohesion and condensation, which is suggested to proceed via formation of SMC rings or assemblies. To learn more about the role of ATP in the architecture of SMC proteins, we report crystal structures of nucleotide-free and ATP bound P. furiosus SMC ATPase domains. ATP dimerizes two SMC ATPase domains by binding to opposing Walker A and signature motifs, indicating that ATP binding can directly assemble SMC proteins. DNA stimulates ATP hydrolysis in the engaged SMC ABC domains, suggesting that ATP hydrolysis can be allosterically regulated. Structural and mutagenesis data identify an SMC protein conserved-arginine finger that is required for DNA stimulation of the ATPase activity and directly connects a putative DNA interaction site to ATP. Our results suggest that stimulation of the SMC ATPase activity may be a specific feature to regulate the ATP-driven assembly and disassembly of SMC proteins.

Selected figure(s)

Figure 2.
Figure 2. ATP Bound Active SiteStereo view of the ATP bound active site, shown as ball-and-stick model with the color code of Figure 1C. Only one out of two symmetrically related composite active sites in the dimer interface is shown. One subunit is depicted in yellow, the other in green. Key side chains are labeled (see text for details), and notable hydrogen bonds are shown as dashed lines. The major dimerization contacts are hydrogen bonds to the ATP γ phosphate from the signature motif and to the ribose 2′- and 3′-OH from K1064 and K1061, respectively. Additional contacts are contributed from the SMC conserved DA box (A1101), which forms a hydrophobic interaction core at the center of the dimerization interface. A water molecule (red sphere) is positioned for collinear attack on the γ phosphate (arrow) by E1098 (mutated to Q in the crystal structure) and the backbone carbonyl of H1102, suggesting that ATP hydrolysis requires the fully engaged ABC dimer.

Figure 3.
Figure 3. ATP-Induced Conformational Changes(A) MAD and 2F[o] − F[c] electron densities (1σ contour) of a portion of the nucleotide free SMCcd crystal structure along with the refined model (color-coded sticks).(B) Superposition of the backbone traces of nucleotide-free (green) and ATP bound (yellow) SMCcd shows that only minor intradomain conformational changes are induced by ATP. The largest conformational changes are observed for the R loop, which is implicated in DNA-stimulated control of ATP hydrolysis, and the C helix, which rotates away to avoid steric clash with the opposing subunit (not shown) and to participate in ABC-ABC interaction. Thus, the predominant role of ATP is probably to control engagement/disengagement of two SMC ABC domains.(C) Detailed view of the R loop (red) of superimposed ATP bound (yellow) and nucleotide-free (gray) SMCcd (shown as backbone worms). R59 (arginine finger) directly hydrogen bonds to the ATP α phosphate (ball-and-stick model). R59 could participate in ATP hydrolysis by compensating the negative charge on the transition state phosphates.(D) Solvent-accessible surface of the ATP bound SMCcd dimer with electrostatic potential (+7 kT/e^− [blue] to −7 kT/e^− [red]). The central region of the composite DNA binding site is formed by the R loop, which is involved in DNA-stimulated activation of ATP hydrolysis. The circled areas represent the location of the coiled-coil domains.

The above figures are reprinted by permission from Cell Press: Curr Biol (2004, 14, 1778-1782) copyright 2004.

Figures were selected by an automated process.