spacer
spacer

PDBsum entry 1fmv

Go to PDB code: 
protein metals links
Contractile protein PDB id
1fmv
Jmol
Contents
Protein chain
743 a.a. *
Metals
_CL
Waters ×601
* Residue conservation analysis
PDB id:
1fmv
Name: Contractile protein
Title: Crystal structure of the apo motor domain of dictyostellium myosin ii
Structure: Myosin ii heavy chain. Chain: a. Fragment: motor domain. Engineered: yes
Source: Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.196     R-free:   0.280
Authors: C.B.Bauer,H.M.Holden,J.B.Thoden,R.Smith,I.Rayment
Key ref:
C.B.Bauer et al. (2000). X-ray structures of the apo and MgATP-bound states of Dictyostelium discoideum myosin motor domain. J Biol Chem, 275, 38494-38499. PubMed id: 10954715 DOI: 10.1074/jbc.M005585200
Date:
18-Aug-00     Release date:   22-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08799  (MYS2_DICDI) -  Myosin-2 heavy chain
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2116 a.a.
743 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     myosin complex   1 term 
  Biochemical function     ATP binding     2 terms  

 

 
DOI no: 10.1074/jbc.M005585200 J Biol Chem 275:38494-38499 (2000)
PubMed id: 10954715  
 
 
X-ray structures of the apo and MgATP-bound states of Dictyostelium discoideum myosin motor domain.
C.B.Bauer, H.M.Holden, J.B.Thoden, R.Smith, I.Rayment.
 
  ABSTRACT  
 
Myosin is the most comprehensively studied molecular motor that converts energy from the hydrolysis of MgATP into directed movement. Its motile cycle consists of a sequential series of interactions between myosin, actin, MgATP, and the products of hydrolysis, where the affinity of myosin for actin is modulated by the nature of the nucleotide bound in the active site. The first step in the contractile cycle occurs when ATP binds to actomyosin and releases myosin from the complex. We report here the structure of the motor domain of Dictyostelium discoideum myosin II both in its nucleotide-free state and complexed with MgATP. The structure with MgATP was obtained by soaking the crystals in substrate. These structures reveal that both the apo form and the MgATP complex are very similar to those previously seen with MgATPgammaS and MgAMP-PNP. Moreover, these structures are similar to that of chicken skeletal myosin subfragment-1. The crystallized protein is enzymatically active in solution, indicating that the conformation of myosin observed in chicken skeletal myosin subfragment-1 is unable to hydrolyze ATP and most likely represents the pre-hydrolysis structure for the myosin head that occurs after release from actin.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon representation of S1dC·MgATP showing the location of MgATP. Figs. 1-4 were prepared with the programs Molscript and Bobscript (37, 26).
Figure 2.
Fig. 2. Stereoview of the difference density for MgATP (a) and the solvent electron density in apoS1dC (b). The location of ATP is shown superimposed on the solvent structure for the apoS1dC. The coefficients used in the calculation were of the form F[o]-F[c] where the substrate and water molecules were removed from the refinement.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 38494-38499) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22343723 B.H.Várkuti, Z.Yang, B.Kintses, P.Erdélyi, I.Bárdos-Nagy, A.L.Kovács, P.Hári, M.Kellermayer, T.Vellai, and A.Málnási-Csizmadia (2012).
A novel actin binding site of myosin required for effective muscle contraction.
  Nat Struct Mol Biol, 19, 299-306.  
22198464 J.C.Cochran, Y.C.Zhao, D.E.Wilcox, and F.J.Kull (2012).
A metal switch for controlling the activity of molecular motor proteins.
  Nat Struct Mol Biol, 19, 122-127.
PDB code: 3pxn
21277856 N.Naber, A.Larson, S.Rice, R.Cooke, and E.Pate (2011).
Multiple conformations of the nucleotide site of Kinesin family motors in the triphosphate state.
  J Mol Biol, 408, 628-642.  
21504733 P.Hooijman, M.A.Stewart, and R.Cooke (2011).
A new state of cardiac myosin with very slow ATP turnover: a potential cardioprotective mechanism in the heart.
  Biophys J, 100, 1969-1976.  
20801044 A.Málnási-Csizmadia, and M.Kovács (2010).
Emerging complex pathways of the actomyosin powerstroke.
  Trends Biochem Sci, 35, 684-690.  
20459085 J.J.Frye, V.A.Klenchin, C.R.Bagshaw, and I.Rayment (2010).
Insights into the importance of hydrogen bonding in the gamma-phosphate binding pocket of myosin: structural and functional studies of serine 236 .
  Biochemistry, 49, 4897-4907.
PDB codes: 3myh 3myk 3myl
19581439 H.Onishi (2009).
Yuji Tonomura: a pioneer in the field of energy transduction in muscle contraction.
  J Biochem, 146, 7.  
19966224 R.V.Agafonov, I.V.Negrashov, Y.V.Tkachev, S.E.Blakely, M.A.Titus, D.D.Thomas, and Y.E.Nesmelov (2009).
Structural dynamics of the myosin relay helix by time-resolved EPR and FRET.
  Proc Natl Acad Sci U S A, 106, 21625-21630.  
19534504 Y.Yang, and Q.Cui (2009).
The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state.
  J Phys Chem A, 113, 12439-12446.  
19756531 Z.Song, K.J.Parker, I.Enoh, H.Zhao, and O.Olubajo (2009).
Myosin-catalyzed ATP hydrolysis elucidated by 31P NMR kinetic studies and 1H PFG-diffusion measurements.
  Anal Bioanal Chem, 395, 1453-1459.  
18854311 B.Kintses, Z.Yang, and A.Málnási-Csizmadia (2008).
Experimental investigation of the seesaw mechanism of the relay region that moves the myosin lever arm.
  J Biol Chem, 283, 34121-34128.  
19325727 I.Aprodu, A.Redaelli, and M.Soncini (2008).
Actomyosin interaction: mechanical and energetic properties in different nucleotide binding States.
  Int J Mol Sci, 9, 1927-1943.  
18725645 J.C.Klein, A.R.Burr, B.Svensson, D.J.Kennedy, J.Allingham, M.A.Titus, I.Rayment, and D.D.Thomas (2008).
Actin-binding cleft closure in myosin II probed by site-directed spin labeling and pulsed EPR.
  Proc Natl Acad Sci U S A, 105, 12867-12872.  
18951904 L.Alamo, W.Wriggers, A.Pinto, F.Bártoli, L.Salazar, F.Q.Zhao, R.Craig, and R.Padrón (2008).
Three-dimensional reconstruction of tarantula myosin filaments suggests how phosphorylation may regulate myosin activity.
  J Mol Biol, 384, 780-797.
PDB code: 3dtp
18568345 M.J.Harris, and H.J.Woo (2008).
Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin.
  Eur Biophys J, 38, 1.  
18765799 R.V.Agafonov, Y.E.Nesmelov, M.A.Titus, and D.D.Thomas (2008).
Muscle and nonmuscle myosins probed by a spin label at equivalent sites in the force-generating domain.
  Proc Natl Acad Sci U S A, 105, 13397-13402.  
18339764 Y.E.Nesmelov, R.V.Agafonov, A.R.Burr, R.T.Weber, and D.D.Thomas (2008).
Structure and dynamics of the force-generating domain of myosin probed by multifrequency electron paramagnetic resonance.
  Biophys J, 95, 247-256.  
18619975 Y.Yang, H.Yu, and Q.Cui (2008).
Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.
  J Mol Biol, 381, 1407-1420.  
17291159 H.Yu, L.Ma, Y.Yang, and Q.Cui (2007).
Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations.
  PLoS Comput Biol, 3, e21.  
17305418 H.Yu, L.Ma, Y.Yang, and Q.Cui (2007).
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues.
  PLoS Comput Biol, 3, e23.  
17900617 S.Tang, J.C.Liao, A.R.Dunn, R.B.Altman, J.A.Spudich, and J.P.Schmidt (2007).
Predicting allosteric communication in myosin via a pathway of conserved residues.
  J Mol Biol, 373, 1361-1373.  
16361336 P.Petrone, and V.S.Pande (2006).
Can conformational change be described by only a few normal modes?
  Biophys J, 90, 1583-1593.  
15897189 X.Liu, S.Shu, M.Kovács, and E.D.Korn (2005).
Biological, biochemical, and kinetic effects of mutations of the cardiomyopathy loop of Dictyostelium myosin II: importance of ALA400.
  J Biol Chem, 280, 26974-26983.  
15184651 D.Risal, S.Gourinath, D.M.Himmel, A.G.Szent-Györgyi, and C.Cohen (2004).
Myosin subfragment 1 structures reveal a partially bound nucleotide and a complex salt bridge that helps couple nucleotide and actin binding.
  Proc Natl Acad Sci U S A, 101, 8930-8935.
PDB codes: 1s5g 1sr6
14747312 G.Li, and Q.Cui (2004).
Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase.
  Biophys J, 86, 743-763.  
14653810 E.Bódis, K.Szarka, M.Nyitrai, and B.Somogyi (2003).
Dynamic reorganization of the motor domain of myosin subfragment 1 in different nucleotide states.
  Eur J Biochem, 270, 4835-4845.  
12885652 M.Nyitrai, W.F.Stafford, A.G.Szent-Györgyi, and M.A.Geeves (2003).
Ionic interactions play a role in the regulatory mechanism of scallop heavy meromyosin.
  Biophys J, 85, 1053-1062.  
12612343 N.Volkmann, G.Ouyang, K.M.Trybus, D.J.DeRosier, S.Lowey, and D.Hanein (2003).
Myosin isoforms show unique conformations in the actin-bound state.
  Proc Natl Acad Sci U S A, 100, 3227-3232.  
14508494 P.D.Coureux, A.L.Wells, J.Ménétrey, C.M.Yengo, C.A.Morris, H.L.Sweeney, and A.Houdusse (2003).
A structural state of the myosin V motor without bound nucleotide.
  Nature, 425, 419-423.
PDB code: 1oe9
14513021 R.S.Goody (2003).
The missing link in the muscle cross-bridge cycle.
  Nat Struct Biol, 10, 773-775.  
14656445 S.Gourinath, D.M.Himmel, J.H.Brown, L.Reshetnikova, A.G.Szent-Györgyi, and C.Cohen (2003).
Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head.
  Structure, 11, 1621-1627.
PDB code: 1qvi
12081502 C.M.Yengo, E.M.De la Cruz, D.Safer, E.M.Ostap, and H.L.Sweeney (2002).
Kinetic characterization of the weak binding states of myosin V.
  Biochemistry, 41, 8508-8517.  
12297624 D.M.Himmel, S.Gourinath, L.Reshetnikova, Y.Shen, A.G.Szent-Györgyi, and C.Cohen (2002).
Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor.
  Proc Natl Acad Sci U S A, 99, 12645-12650.
PDB codes: 1kk7 1kk8 1kqm 1kwo 1l2o
12499355 S.Burgess, M.Walker, F.Wang, J.R.Sellers, H.D.White, P.J.Knight, and J.Trinick (2002).
The prepower stroke conformation of myosin V.
  J Cell Biol, 159, 983-991.  
11297926 A.Houdusse, and H.L.Sweeney (2001).
Myosin motors: missing structures and hidden springs.
  Curr Opin Struct Biol, 11, 182-194.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.