PDBsum entry 2aka

Contractile protein

PDB id: 2aka

Contents

Protein chains

764 a.a.

299 a.a.

Ligands

THR-ARG-LEU-VAL-PRO-ARG

Waters ×754

References listed in PDB file

Key reference

Title

Crystal structure of the gtpase domain of rat dynamin 1.

Authors

T.F.Reubold, S.Eschenburg, A.Becker, M.Leonard, S.L.Schmid, R.B.Vallee, F.J.Kull, D.J.Manstein.

Ref.

Proc Natl Acad Sci U S A, 2005, 102, 13093-13098. [DOI no: 10.1073/pnas.0506491102]

PubMed id

16141317

Abstract

Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases. Two highly conserved arginines, Arg-66 and Arg-67, greatly restrict the mobility of switch I and are ideally positioned to relay information about the nucleotide state to other parts of the protein. Our results support a model in which switch I residue Arg-59 gates GTP binding in an assembly-dependent manner and the GTPase effector domain functions as an assembly-dependent GTPase activating protein in the fashion of RGS-type GAPs.

Figure 3.
Fig. 3. Stabilization of the switch motifs (stereo view). P-loop and switch elements are colored as in Fig. 2, and B and 2A are shown in light gray. Side chains and carbonyl groups are shown as stick models, and main-chain nitrogens are shown as blue spheres. Polar and ionic interactions are drawn as dotted lines.

Figure 5.
Fig. 5. Docking of the C-terminal myosin helix into the hydrophobic groove of dynamin. (A) The structure of the dynamin 1-myosin fusion as solid cartoon with the dynamin 1 GTPase domain drawn in dark gray, the groove helices A and 5 in yellow and orange, respectively, and the myosin motor domain in blue. The structure of the dynamin A fusion is superimposed in transparent gray. Although the dynamin domains align well, the myosin motor domains adopt different conformations in the dynamin 1 and dynamin A fusion structures. (B) Schematic representation of the hydrophobic interactions (solid lines between the respective amino acid partners) between helices A (yellow box) and 5 (orange box) and the C-terminal myosin helix (blue box).

Secondary reference #1

Title

A structural model for actin-Induced nucleotide release in myosin.

Authors

T.F.Reubold, S.Eschenburg, A.Becker, F.J.Kull, D.J.Manstein.

Ref.

Nat Struct Biol, 2003, 10, 826-830. [DOI no: 10.1038/nsb987]

PubMed id

14502270

Figure 2.
Figure 2. Global conformational changes in the O/O conformation of myosin II. (a) Ribbon diagram of the nucleotide-free structure indicating the subdomains of the myosin motor. (b) P-loop superposition of the three myosin conformations shows the movement of the 50K domain with respect to the rest of the molecule. C/C, blue; C/O, black; O/O, red. Orientation as in a. Dashed lines indicate distance between identical residues in the three conformations (Gly401 in the cardiomyopathy loop and Asn537 in the helix-turn-helix motif). (c) Superposition of the upper 50K domains reveals large differences with respect to the position of the lower 50K domain. (d) Changes in the orientation of three edge -strands results in the global changes shown in b and c. P-loop superposition was used with a similar orientation to that in b. Five core strands are shown for the C/O (gray) and O/O (red) conformations. The left-most two strands remain closely overlapping over their entire lengths, whereas the three strands on the right diverge substantially at the top of the sheet while remaining in the same position at the bottom. P, strand preceding the P-loop; SwII, strand preceding the switch-II loop; SwI, strand following switch I. The ADP is shown from the C/O structure for reference. The asterisks in a and b mark the P-loop.

Figure 3.
Figure 3. Structural model for the actin-activated myosin II ATPase cycle.

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd