2BL0

Physarum polycephalum myosin II regulatory domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Evidence for Non-Canonical Binding of Ca2+ to a Canonical EF-Hand of a Conventional Myosin.

Debreczeni, J.E.Farkas, L.Harmat, V.Hetenyi, C.Hajdu, I.Zavodszky, P.Kohama, K.Nyitray, L.

(2005) J.Biol.Chem. 280: 41458

  • DOI: 10.1074/jbc.M506315200

  • PubMed Abstract: 
  • We have previously identified a single inhibitory Ca2+-binding site in the first EF-hand of the essential light chain of Physarum conventional myosin (Farkas, L., Malnasi-Csizmadia, A., Nakamura, A., Kohama, K., and Nyitray, L. (2003) J. Biol. Chem. ...

    We have previously identified a single inhibitory Ca2+-binding site in the first EF-hand of the essential light chain of Physarum conventional myosin (Farkas, L., Malnasi-Csizmadia, A., Nakamura, A., Kohama, K., and Nyitray, L. (2003) J. Biol. Chem. 278, 27399-27405). As a general rule, conformation of the EF-hand-containing domains in the calmodulin family is "closed" in the absence and "open" in the presence of bound cations; a notable exception is the unusual Ca2+-bound closed domain in the essential light chain of the Ca2+-activated scallop muscle myosin. Here we have reported the 1.8 A resolution structure of the regulatory domain (RD) of Physarum myosin II in which Ca2+ is bound to a canonical EF-hand that is also in a closed state. The 12th position of the EF-hand loop, which normally provides a bidentate ligand for Ca2+ in the open state, is too far in the structure to participate in coordination of the ion. The structure includes a second Ca2+ that only mediates crystal contacts. To reveal the mechanism behind the regulatory effect of Ca2+, we compared conformational flexibilities of the liganded and unliganded RD. Our working hypothesis, i.e. the modulatory effect of Ca2+ on conformational flexibility of RD, is in line with the observed suppression of hydrogen-deuterium exchange rate in the Ca2+-bound form, as well as with results of molecular dynamics calculations. Based on this evidence, we concluded that Ca2+-induced change in structural dynamics of RD is a major factor in Ca2+-mediated regulation of Physarum myosin II activity.


    Organizational Affiliation

    Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR PLASMODIAL MYOSIN HEAVY CHAIN
A
63Physarum polycephalumMutation(s): 0 
Gene Names: mynP1
Find proteins for Q9BJD3 (Physarum polycephalum)
Go to UniProtKB:  Q9BJD3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MYOSIN REGULATORY LIGHT CHAIN
B
145Physarum polycephalumMutation(s): 0 
Find proteins for P08053 (Physarum polycephalum)
Go to UniProtKB:  P08053
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MYOSIN REGULATORY LIGHT CHAIN
C
142Physarum polycephalumMutation(s): 0 
Gene Names: RMLC
Find proteins for Q8WSQ4 (Physarum polycephalum)
Go to UniProtKB:  Q8WSQ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.574α = 90.00
b = 70.858β = 90.00
c = 97.877γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
DMphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance