1VOM

COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution.

Smith, C.A.Rayment, I.

(1996) Biochemistry 35: 5404-5417

  • DOI: 10.1021/bi952633+

  • PubMed Abstract: 
  • The structure of the vanadate-trapped ADP complex of a truncated head of Dictyostelium myosin II consisting of residues Asp 2-Asn 762 has been determined by molecular replacement at 1.9 A resolution and refined to a crystallographic R-factor of 19.4% ...

    The structure of the vanadate-trapped ADP complex of a truncated head of Dictyostelium myosin II consisting of residues Asp 2-Asn 762 has been determined by molecular replacement at 1.9 A resolution and refined to a crystallographic R-factor of 19.4%. The crystals belong to the orthorhombic space group C2221 where a = 84.50 A, b = 145.4 A, and c = 152.8 A. The conformation of the protein is similar to that of MgADP.AlF4.SlDc [Fisher, A.J., et al. (1995) Biochemistry 34, 8960-8972]. The nucleotide binding site contains a complex between MgADP and vanadate where MgADP exhibits a very similar conformation to that seen in previous complexes. The vanadate ion adopts a trigonal bipyramidal coordination. The three equatorial oxygen ligands are fairly short, average 1.7 A, relative to a single bond distance of approximately 1.8 A and are coordinated to the magnesium ion, N zeta of Lys 185, and five other protein ligands. The apical coordination to the vanadate ion is filled by a terminal oxygen on the beta-phosphate of ADP and a water molecule at bond distances of 2.1 and 2.3 A, respectively. The long length of the apical bonds suggests that the bond order is considerably less than unity. This structure confirms the earlier suggestion that vanadate is a model for the transition state of ATP hydrolysis and thus provides insight into those factors that are responsible for catalysis. In particular, it shows that the protein ligands and water structure surrounding the gamma-phosphate pocket are oriented to stabilize a water molecule in an appropriate position for in-line nucleophilic attack on the gamma-phosphorus of ATP. This structure reveals also an orientation of the COOH-terminal region beyond Thr 688 which is very different from that observed in either MgADP.BeFx.SlDc or chicken skeletal myosin subfragment 1. This is consistent with the COOH-terminal region of the molecule playing an important role in the transduction of chemical energy of hydrolysis of ATP into mechanical movement.


    Related Citations: 
    • X-Ray Structures of the Myosin Motor Domain of Dictyostelium Discoideum Complexed with Mgadp.Befx and Mgadp.Alf4-
      Fisher, A.J.,Smith, C.A.,Thoden, J.B.,Smith, R.,Sutoh, K.,Holden, H.M.,Rayment, I.
      (1995) Biochemistry 34: 8960
    • Three-Dimensional Structure of Myosin Subfragment-1: A Molecular Motor
      Rayment, I.,Rypniewski, W.R.,Schmidt-Base, K.,Smith, R.,Tomchick, D.R.,Benning, M.M.,Winkelmann, D.A.,Wesenberg, G.,Holden, H.M.
      (1993) Science 261: 50
    • Structural Studies of Myosin:Nucleotide Complexes: A Revised Model for the Molecular Basis of Muscle Contraction
      Fisher, A.J.,Smith, C.A.,Thoden, J.,Smith, R.,Sutoh, K.,Holden, H.M.,Rayment, I.
      (1995) Biophys.J. 68: 19S
    • Force-Generating Domain of Myosin Motor
      Itakura, S.,Yamakawa, H.,Toyoshima, Y.Y.,Ishijima, A.,Kojima, T.,Harada, Y.,Yanagida, T.,Wakabayashi, T.,Sutoh, K.
      (1993) Biochem.Biophys.Res.Commun. 196: 1504


    Organizational Affiliation

    Institute for Enzyme Research, University of Wisconsin, Madison 53705, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYOSIN
A
762Dictyostelium discoideumGene Names: mhcA
Find proteins for P08799 (Dictyostelium discoideum)
Go to UniProtKB:  P08799
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
VO4
Query on VO4

Download SDF File 
Download CCD File 
A
VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.500α = 90.00
b = 145.400β = 90.00
c = 153.800γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance