The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB

Abstract

MukB, a divergent structural maintenance of chromosomes (SMC) protein, is important for chromosomal segregation and condensation in gamma-proteobacteria. MukB and canonical SMC proteins share a characteristic five-domain structure. Globular N- and C-terminal domains interact to form an ATP-binding cassette-like ATPase or "head" domain, which is connected to a smaller dimerization or "hinge" domain by a long, antiparallel coiled coil. In addition to mediating dimerization, this hinge region has been implicated in both conformational flexibility and dynamic protein-DNA interactions. We report here the first crystallographic model of the MukB hinge domain. This model also contains approximately 20% of the coiled-coil domain, including an unusual coiled-coil deviation. These results will facilitate studies to clarify the roles of both the hinge and the coiled-coil domains in MukB function.

Fig 1

Overall structure of MukB-D (566–863). Each MukB-D monomer contains the complete hinge domain (666–779) and two coiled coil strands (572–665 and 780–854). The angle of the V-shaped dimer is ~ 120°. The length of coiled coil domain in each monomer is ~ 100 Å. The hinge domains of two monomers are colored green and magenta respectively; the coiled coil domains for the same monomers are colored light blue and blue respectively. All figures involving crystal structures were prepared with PyMol (DeLano Scientific LLC). Experimental details for protein crystallization and structure determination are included in the supplementary material.

Fig 2

Secondary structural features of E. coli MukB and TmSMC hinge domain. (A) Highlighted view of the shared features (magenta) between MukB and TmSMC. (B) Comparison of the major dimerization interfaces in MukB and TmSMC. Two monomers from the same dimer are labeled as green and magenta respectively.

Fig 3

Comparison of E. coli MukB and TmSMC hinge domains. Color coding is the same as in Fig 1. (A) The MukB hinge domain has an overall shape different from the “donut” shaped TmSMC hinge domain. View is from the upper face of Fig 1. Two water molecules in MukB dimer interface are shown as yellow spheres (inset). (B) Surface potential analysis of MukB and TmSMC, generated by APBS. Views are from the inner (bottom) and upper faces of Fig 1. Positively-charged regions are colored blue, while negatively-charged regions are colored red.

Fig 3

Comparison of E. coli MukB and TmSMC hinge domains. Color coding is the same as in Fig 1. (A) The MukB hinge domain has an overall shape different from the “donut” shaped TmSMC hinge domain. View is from the upper face of Fig 1. Two water molecules in MukB dimer interface are shown as yellow spheres (inset). (B) Surface potential analysis of MukB and TmSMC, generated by APBS. Views are from the inner (bottom) and upper faces of Fig 1. Positively-charged regions are colored blue, while negatively-charged regions are colored red.

Fig 4

Register analysis of coiled coil domain in E. coli MukB. (A) Close-up view of the coiled coil segment highlighting inter-strand packing (top) and the coiled coil discontinuity (bottom). The N- and C-terminal helical strands within the same monomer are colored light blue and green respectively. The coiled coil regions were assigned by the computer algorithm SOCKET (packing cut-off = 7.4 Å). The two regions of the coiled coil are denoted CC3 (583–601 and 834–852) and CC4 (632–663 and 787–818). The side chains of residues at a (red) and d (dark blue) positions are shown as sticks. (B) Sequence of coiled coil strands highlighting residues involved in inter-strand packing interactions.