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

* Residue conservation analysis

PDB id:

2aka

Name:

Contractile protein

Title:

Structure of the nucleotide-free myosin ii motor domain from dictyostelium discoideum fused to the gtpase domain of dynamin 1 from rattus norvegicus

Structure:

Myosin ii heavy chain. Chain: a. Engineered: yes. Other_details: fused to a linker and dynamin-1. Linker. Chain: l. Engineered: yes. Other_details: links myosin and dynamin. Dynamin-1.

Source:

Dictyostelium discoideum. Organism_taxid: 44689. Gene: mhca. Expressed in: dictyostelium discoideum. Expression_system_taxid: 44689. Synthetic: yes. Other_details: synthetic linker. Rattus norvegicus. Norway rat.

Biol. unit:

Trimer (from PQS)

Resolution:

1.90Å R-factor: 0.185 R-free: 0.224

Authors:

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

Key ref:

T.F.Reubold et al. (2005). Crystal structure of the GTPase domain of rat dynamin 1. Proc Natl Acad Sci U S A, 102, 13093-13098. PubMed id: 16141317 DOI: 10.1073/pnas.0506491102

Date:

03-Aug-05 Release date: 23-Aug-05

Protein chain

P08799  (MYS2_DICDI) -  Myosin-2 heavy chain from Dictyostelium discoideum

Seq: 2116 a.a.

Struc: 764 a.a.

Protein chain

P21575  (DYN1_RAT) -  Dynamin-1 from Rattus norvegicus

Seq: 864 a.a.

Struc: 299 a.a.

Enzyme reactions

• Enzyme class: Chain B: E.C.3.6.5.5 - dynamin GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0506491102

Proc Natl Acad Sci U S A 102:13093-13098 (2005)

PubMed id: 16141317

Crystal structure of the GTPase domain of rat dynamin 1.

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

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.

Selected figure(s)

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).

Figures were selected by an automated process.