PDBsum entry 3euk

Cell cycle

PDB id: 3euk

Contents

Protein chains

442 a.a. *

455 a.a. *

101 a.a. *

124 a.a. *

173 a.a. *

107 a.a. *

Ligands

AGS ×4

Metals

_MG ×4

* Residue conservation analysis

PDB id:

3euk

Name:

Cell cycle

Title:

Crystal structure of muke-mukf(residues 292-443)-mukb(head domain)- atpgammas complex, asymmetric dimer

Structure:

Chromosome partition protein mukb, linker. Chain: a, c, f, h. Fragment: head domain. Synonym: structural maintenance of chromosome-related protein. Engineered: yes. Mutation: yes. Chromosome partition protein mukf. Chain: e, j. Fragment: residues 292-443.

Source:

Haemophilus ducreyi (strain 35000hp / atcc 700724). Organism_taxid: 233412. Gene: mukb, hd_1582. Expressed in: escherichia coli. Expression_system_taxid: 562. Haemophilus ducreyi. Organism_taxid: 730. Gene: mukf, hd_1585.

Resolution:

4.00Å R-factor: 0.271 R-free: 0.324

Authors:

J.S.Woo,J.H.Lim,H.C.Shin,B.H.Oh

Key ref:

J.S.Woo et al. (2009). Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions. Cell, 136, 85-96. PubMed id: 19135891 DOI: 10.1016/j.cell.2008.10.050

Date:

10-Oct-08 Release date: 20-Jan-09

Protein chain

Q7VL96  (MUKB_HAEDU) -  Chromosome partition protein MukB from Haemophilus ducreyi (strain 35000HP / ATCC 700724)

Seq: 1503 a.a.

Struc: 442 a.a.*

Protein chains

Q7VL96  (MUKB_HAEDU) -  Chromosome partition protein MukB from Haemophilus ducreyi (strain 35000HP / ATCC 700724)

Seq: 1503 a.a.

Struc: 455 a.a.*

Protein chain

Q7VL94  (MUKF_HAEDU) -  Chromosome partition protein MukF from Haemophilus ducreyi (strain 35000HP / ATCC 700724)

Seq: 443 a.a.

Struc: 101 a.a.*

Protein chain

Q7VL94  (MUKF_HAEDU) -  Chromosome partition protein MukF from Haemophilus ducreyi (strain 35000HP / ATCC 700724)

Seq: 443 a.a.

Struc: 124 a.a.*

Protein chain

Q7VL95  (MUKE_HAEDU) -  Chromosome partition protein MukE from Haemophilus ducreyi (strain 35000HP / ATCC 700724)

Seq: 238 a.a.

Struc: 173 a.a.

Protein chain

Q7VL95  (MUKE_HAEDU) -  Chromosome partition protein MukE from Haemophilus ducreyi (strain 35000HP / ATCC 700724)

Seq: 238 a.a.

Struc: 107 a.a.*

* PDB and UniProt seqs differ at 434 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C, E, F, H, J, L, M: E.C.?

DOI no: 10.1016/j.cell.2008.10.050

Cell 136:85-96 (2009)

PubMed id: 19135891

Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions.

J.S.Woo, J.H.Lim, H.C.Shin, M.K.Suh, B.Ku, K.H.Lee, K.Joo, H.Robinson, J.Lee, S.Y.Park, N.C.Ha, B.H.Oh.

ABSTRACT

Condensins are key mediators of chromosome condensation across organisms. Like other condensins, the bacterial MukBEF condensin complex consists of an SMC family protein dimer containing two ATPase head domains, MukB, and two interacting subunits, MukE and MukF. We report complete structural views of the intersubunit interactions of this condensin along with ensuing studies that reveal a role for the ATPase activity of MukB. MukE and MukF together form an elongated dimeric frame, and MukF's C-terminal winged-helix domains (C-WHDs) bind MukB heads to constitute closed ring-like structures. Surprisingly, one of the two bound C-WHDs is forced to detach upon ATP-mediated engagement of MukB heads. This detachment reaction depends on the linker segment preceding the C-WHD, and mutations on the linker restrict cell growth. Thus ATP-dependent transient disruption of the MukB-MukF interaction, which creates openings in condensin ring structures, is likely to be a critical feature of the functional mechanism of condensins.

Selected figure(s)

Figure 3.
Figure 3. Formation of the Asymmetric hMukE–hMukF(M+C)–(hMukBhd^EQ–ATPγS)[2] Dimer
(A) Structure of the asymmetric dimer in the Form II crystal. Only one C-WHD of hMukF is bound to dimerized MukB heads. In the inset, the 2F[o]-F[c] map calculated with the final refined model highlights the electron density for the linker segment preceding α1.
(B) Structural superposition. The C-WHDs of MukF in the asymmetric dimer (red) and the symmetric dimer (pink) in the Form I crystal are superposed. A circle highlights that α1 in the asymmetric dimer is longer than that in the symmetric dimer. The linker segment in the asymmetric dimer overlaps with one MukF C-WHD in the symmetric dimer.
(C) Detachment of hMukE–hMukF(M+C) from dimerized MukB heads in solution. A sample containing 4 μM hMukE–hMukF(M+C)–hMukBhd^EQ (band a) was reacted with 2 mM ATP and visualized on a native gel. The mixture was partially separated with a Superdex 200 column, and the chromatogram is shown along with the size marker positions. The eluted fractions, indicated by a double-headed arrow, were visualized on a native and a denaturing gel, showing that bands b and c correspond to high- and low-molecular weight species, respectively. Band c is assigned to detached hMukE–hMukF(M+C) according to the same band position of purified hMukE–hMukF(M+C) (labeled as “Con”). By subtraction, band b is assigned to hMukE–hMukF(M+C)–(hMukBhd^EQ–ATP)[2], which was confirmed by quantification of the band intensities for lane 1 of the denaturing gel ([hMukBhd^EQ]/[hMukE dimer] = vert, similar 1.7). Accordingly, the minor species present in the unreacted sample is identified as copurified asymmetric dimer resulting from very low catalytic activity of hMukBhd^EQ. The observed conversion reaction is schematically illustrated.
(D) Control experiments. Triple complexes between MukE, MukF(M+C) and the indicated head domain of MukB were analyzed by native gel electrophoresis. Left: Catalytically active MukE–MukF(M+C)–MukBhd in reacting with 2 mM AMPPNP produced the conversion products observed in C. Middle: In the presence of 2 mM ATP, the conversion reaction was observed with the MukBhd^EQ-containing complex, but not with the MukBhd^SR-containing complex. Right: Conversion of the triple complexes containing the indicated MukB head did not take place, when incubated without ATP.

Figure 7.
Figure 7. Heterogeneity, Head Domain Contacts and Opening of the MukBEF Ring Structures
(A) Architectural heterogeneity. Three examples of closed ring structures, including MukB–MukEF are schematically drawn. The portion enclosed in the dotted box is presented in ribbon drawing in the inset.
(B) Effect of MukEF on contacts between MukB heads. The MukEF frame in MukB–MukEF prohibits intracomplex head domain contact. Diffusional, intercomplex-wise head domain contact should be infrequent (left). The MukEF frame in a higher-order complex restricts free diffusion of MukB heads and their contacts within the complex can be frequent (right).
(C) Ring opening. Opening of the closed ring structures via intercomplex and intracomplex head domain engagement is illustrated. The arrows indicate contacts for head domain engagement. The portion of the two MukB–MukEF rings enclosed in the dotted box is presented in ribbon drawing in the inset. One of the two rings (left) has an opening between its MukB head and MukF C-WHD. The architectures of MukB–MukEF in the insets in A and C were constructed based on the presented structures.

The above figures are reprinted by permission from Cell Press: Cell (2009, 136, 85-96) copyright 2009.

Figures were selected by an automated process.