PDBsum entry 3h4s

Motor protein/calcium binding protein

PDB id: 3h4s

Contents

Protein chains

359 a.a. *

96 a.a. *

Ligands

ADP

Metals

_MG ×2

_CA

Waters ×160

* Residue conservation analysis

PDB id:

3h4s

Name:

Motor protein/calcium binding protein

Title:

Structure of the complex of a mitotic kinesin with its calcium binding regulator

Structure:

Kinesin-like calmodulin-binding protein. Chain: a. Fragment: unp residues 875-1260. Engineered: yes. Mutation: yes. Kcbp interacting ca2+-binding protein. Chain: e. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress,thale-cress. Organism_taxid: 3702. Gene: at5g65930. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: kic. Expression_system_taxid: 562

Resolution:

2.40Å R-factor: 0.223 R-free: 0.228

Authors:

M.V.Vinogradova

Key ref:

M.V.Vinogradova et al. (2009). Structure of the complex of a mitotic kinesin with its calcium binding regulator. Proc Natl Acad Sci U S A, 106, 8175-8179. PubMed id: 19416847 DOI: 10.1073/pnas.0811131106

Date:

20-Apr-09 Release date: 19-May-09

Protein chain

Q9FHN8  (KN14E_ARATH) -  Kinesin-like protein KIN-14E from Arabidopsis thaliana

Seq: 1260 a.a.

Struc: 359 a.a.*

Protein chain

Q9ZPX9  (KIC_ARATH) -  Calcium-binding protein KIC from Arabidopsis thaliana

Seq: 135 a.a.

Struc: 96 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1073/pnas.0811131106

Proc Natl Acad Sci U S A 106:8175-8179 (2009)

PubMed id: 19416847

Structure of the complex of a mitotic kinesin with its calcium binding regulator.

M.V.Vinogradova, G.G.Malanina, A.S.Reddy, R.J.Fletterick.

ABSTRACT

Much of the transport, tension, and movement in mitosis depends on kinesins, the ATP-powered microtubule-based motors. We report the crystal structure of a kinesin complex, the mitotic kinesin KCBP bound to its principal regulator KIC. Shown to be a Ca(2+) sensor, KIC works as an allosteric trap. Extensive intermolecular interactions with KIC stabilize kinesin in its ADP-bound conformation. A critical component of the kinesin motile mechanism, called the neck mimic, switches its association from kinesin to KIC, stalling the motor. KIC denies access of the motor to its track by steric interference. Two major features of this regulation, allosteric trapping and steric blocking, are likely to be general for all kinesins.

Selected figure(s)

Figure 1.
Three-dimensional organization of complex between kinesin motor KCBP and regulatory Ca^2+-binding protein KIC. (A) Schematic illustration of complex components. The fragments of KCBP and KIC visualized in the crystal structure are traced in orange for KCBP and in green for KIC. The domain structure of KCBP is depicted. (B) Crystal structure of the complex of kinesin KCBP and KIC solved at a resolution of 2.4 Å. The motor (light orange) and KIC (green) are shown schematically. ADP (light blue) and Ca^2+ ion (black) are space-filling models. The regulatory domain of KCBP is highlighted in orange. (C and D) Two views of the structure of KIC in the complex. In C, KIC is shown in orientation allowing visualization of the part corresponding to the central helix of the Ca^2+ sensors (calmodulin, troponin C). The C-terminal part of the “central” helix in KIC is less ordered than its N-terminal half. For alignment of KIC with troponin C and calmodulin, please see Table S2. In D, the EF-hands helices are indicated (A, B, C, D) as the similar elements in the structures of Ca^2+ sensors. The β-sheet stabilizing the EF-hand pair is shown in cyan.

Figure 4.
The conformational change in KCBP accompanying ATP hydrolysis. (A) The structure of KCBP-KIC complex is superposed with the structure of KCBP alone (PDB ID code 3cob, chain A). Only the switch II helix α4 and the regulatory elements (in pink) of the solo KCBP structure are shown. The analogous elements of KCBP in the structure of the complex are highlighted in orange. For our previous crystallographic studies of KCBP (PDB ID codes 1sdm, 3cob, 3cnz), we used KCBP from potato (amino acids 884-1252) that is 80% identical to Arabidopsis KCBP. (B) The hydrophobic pocket (marked in yellow) on the kinesin surface (gray) is occupied by Ile-1210 in the ATP-like conformation. (C) The shifted hydrophobic pocket (marked in yellow) on the kinesin surface (gray) is occupied by Ile-890 of the β1 strand as found in the ADP state. Ile-1210 is expelled from the hydrophobic pocket on the kinesin surface and interacts with KIC (Fig. 3). Hydrophobic residues are conserved at positions 890 and 1210 in all kinesins. Helices α4 and α6 and the β1 strand of KCBP (indicated) are shown schematically and are visible through the translucent surface. The neck mimic is shown as a coil and is colored according to the conformational state.

Figures were selected by the author.

Author's comment

Here we report the first crystal structure of any kinesin in complex with its specific protein regulator. This is the plant mitotic kinesin, KCBP, bound to a Ca2+ ion sensing protein, KIC. KIC abolishes binding of this kinesin to microtubules and inhibits its microtubule-stimulated ATP hydrolysis. The structure reveals KIC to be a unique Ca2+-sensor of the calmodulin family that has a surprisingly sufficient “half-calmodulin”- like fold. Despite the sequence prediction of the only Ca2+ ion binding structural motif (EF-hand), KIC contains two of them. The amino acid composition of one does not support Ca2+ ion binding, though its conformation is nearly identical to the second that binds Ca2+ ion. Both are fully “open” to allow binding of the special target helix of kinesin in an exposed hydrophobic pocket. The interface between KIC and kinesin comprises nearly 2000 Å and extends well beyond the helix in the pocket. The newly observed interface of the Ca2+-sensor and its target is designed to recognize a particular conformation of the regulated target. The extensive intermolecular interactions with KIC specifically complement and stabilize kinesin in its ADP-bound conformation. The conserved element of kinesin motility, termed neck linker in N-terminal kinesins and “neck mimic” in C-terminal kinesins, is captured by KIC binding. We suggest that the mechanism for blocking kinesin by KIC is multi- channelled. Sequestering the “neck mimic” by KIC prevents the motor from adopting the conformational state needed for ATP binding, i.e. KIC works as an allosteric trap. Modelled on microtubules, KIC bound in this manner would produce steric clashes with microtubules, denying the motor access to its track.
Maia V Vinogradova