PDBsum entry 3dc4

Motor protein

PDB id: 3dc4

Contents

Protein chain

291 a.a. *

Ligands

ADP

Metals

_MG

Waters ×312

* Residue conservation analysis

PDB id:

3dc4

Name:

Motor protein

Title:

Crystal structure of the drosophila kinesin family member nod in complex with adp

Structure:

Kinesin-like protein nod. Chain: a. Fragment: catalytic core domain (residues 1-318). Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: nod, noda, cg1763. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.227 R-free: 0.255

Authors:

J.C.Cochran,N.K.Mulko,F.J.Kull

Key ref:

J.C.Cochran et al. (2009). ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement. Cell, 136, 110-122. PubMed id: 19135893 DOI: 10.1016/j.cell.2008.11.048

Date:

03-Jun-08 Release date: 10-Feb-09

Protein chain

P18105  (NOD_DROME) -  Kinesin-like protein Nod from Drosophila melanogaster

Seq: 666 a.a.

Struc: 291 a.a.*

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

DOI no: 10.1016/j.cell.2008.11.048

Cell 136:110-122 (2009)

PubMed id: 19135893

ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement.

J.C.Cochran, C.V.Sindelar, N.K.Mulko, K.A.Collins, S.E.Kong, R.S.Hawley, F.J.Kull.

ABSTRACT

Segregation of nonexchange chromosomes during Drosophila melanogaster meiosis requires the proper function of NOD, a nonmotile kinesin-10. We have determined the X-ray crystal structure of the NOD catalytic domain in the ADP- and AMPPNP-bound states. These structures reveal an alternate conformation of the microtubule binding region as well as a nucleotide-sensitive relay of hydrogen bonds at the active site. Additionally, a cryo-electron microscopy reconstruction of the nucleotide-free microtubule-NOD complex shows an atypical binding orientation. Thermodynamic studies show that NOD binds tightly to microtubules in the nucleotide-free state, yet other nucleotide states, including AMPPNP, are weakened. Our pre-steady-state kinetic analysis demonstrates that NOD interaction with microtubules occurs slowly with weak activation of ADP product release. Upon rapid substrate binding, NOD detaches from the microtubule prior to the rate-limiting step of ATP hydrolysis, which is also atypical for a kinesin. We propose a model for NOD's microtubule plus-end tracking that drives chromosome movement.

Selected figure(s)

Figure 1.
Figure 1. X-Ray Crystal Structure of NOD•ADP and NOD•AMPPNP
(A) Structure of NOD•ADP is shown. ADP is displayed as a ball-and-stick model.
(B) NOD•AMPPNP is shown as in (A).
(C and D) Superposition of NOD•ADP (blue) and NOD•AMPPNP (orange) through alignment of the P loop (G87-S94) as viewed from the top (C) and from the side (D). Arrows highlight the differences between the two states in Sw1, Sw2, α3, and L11.
(E) Configuration of hydrogen bonds between Sw1/Sw2 residues in NOD•ADP. Hydrogen bonds with measured distances are highlighted with magenta dashed lines. The water molecules that coordinate Mg^2+ are shown as red spheres.
(F) Active site configuration of hydrogen bonds for NOD•AMPPNP in a similar orientation as (E).

Figure 2.
Figure 2. L5 and MT Binding Region in NOD Show Unique Conformation Compared to Other Kinesins
(A) Comparison of L5 in different kinesin families (gray) after P loop superposition. The N-terminal half of L5 in NOD (blue) packs against α3.
(B) Detailed view of L5 in NOD (blue) compared to L5 in kinesin-5 (orange) bound to monastrol (Mon). The pocket formed by P101 and P102 on L5 and L180, H181, and L184 on α3 is shown.
(C) NOD•ADP (blue) was superposed with KHC•ADP (gold) and oriented to show the β5-L8 lobe.
(D–F) NOD's “Sw2 cluster” (blue) is compared to the “ADP-like” conformation in kinesin-1 ([D], 1bg2, magenta), the “ATP-like” conformation in kinesin-1 ([E], 1mkj, gold), and KIF2C ([F], 1v8j, red). View is from the MT binding surface. Clockwise rotation of NOD's α4 relative to kinesin-1's α4 is highlighted in (D) and (E).

The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2009, 136, 110-122) copyright 2009.

Figures were selected by an automated process.