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PDBsum entry 1lvk

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protein ligands metals links
Contractile protein PDB id
1lvk
Jmol
Contents
Protein chain
743 a.a. *
Ligands
MNT-BEF
Metals
_MG
Waters ×2
* Residue conservation analysis
PDB id:
1lvk
Name: Contractile protein
Title: X-ray crystal structure of the mg (dot) 2'(3')-o-(n- methylanthraniloyl) nucleotide bound to dictyostelium discoideum myosin motor domain
Structure: Myosin. Chain: a. Fragment: motor domain. Engineered: yes. Mutation: yes. Other_details: genetically truncated head of myosin from dictyostelium
Source: Dictyostelium discoideum. Organism_taxid: 44689. Expressed in: dictyostelium discoideum. Expression_system_taxid: 44689
Resolution:
1.90Å     R-factor:   0.200    
Authors: C.B.Bauer,P.A.Kuhlman,C.R.Bagshaw,I.Rayment
Key ref:
C.B.Bauer et al. (1997). X-ray crystal structure and solution fluorescence characterization of Mg.2'(3')-O-(N-methylanthraniloyl) nucleotides bound to the Dictyostelium discoideum myosin motor domain. J Mol Biol, 274, 394-407. PubMed id: 9405148 DOI: 10.1006/jmbi.1997.1325
Date:
05-Sep-97     Release date:   28-Jan-98    
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  CATH domain
* PDB and UniProt seqs differ at 12 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: 10.1006/jmbi.1997.1325 J Mol Biol 274:394-407 (1997)
PubMed id: 9405148  
 
 
X-ray crystal structure and solution fluorescence characterization of Mg.2'(3')-O-(N-methylanthraniloyl) nucleotides bound to the Dictyostelium discoideum myosin motor domain.
C.B.Bauer, P.A.Kuhlman, C.R.Bagshaw, I.Rayment.
 
  ABSTRACT  
 
Mant (2'(3')-O-(N-methylanthraniloyl)) labeled nucleotides have proven to be useful tools in the study of the kinetic mechanism of the myosin ATPase by fluorescence spectroscopy. The sensitivity of the mant fluorophore to its local environment also makes it suitable to investigate the exposure of bound nucleotides to solvent from collisional quenching measurements. Here we present the crystal structure of mant-ADP and beryllium fluoride complexed with Dictyostelium discoideum myosin motor domain (S1dC) at 1.9 A resolution. We complement the structural approach with an investigation of the accessibility of the mant moiety to solvent using acrylamide quenching of fluorescence emission. In contrast to rabbit skeletal myosin subfragment 1, where the mant group is protected from acrylamide (Ksv=0.2 M-1), the fluorophore is relatively exposed when bound to Dictyostelium myosin motor domain (Ksv= 1.4 M-1). Differences between the Dictyostelium structure and that of vertebrate skeletal subfragment 1, in the region of the nucleotide binding pocket, are proposed as an explanation for the differences observed in the solvent accessibility of complexed mant-nucleotides. We conclude that protection of the mant group from acrylamide quenching does not report on overall closure of the nucleotide binding pocket but reflects more local structural changes.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Stereo ribbon representation of the portion of S1dC heavy chain which is in close contact with the mant ring. The side-chains which make contacts with the mant ring of less than 5.0 Å are shown with yellow bonds for the S1dC complex. The corresponding side-chains for chicken S1 are shown with thin black bonds. Residues labeled with their three letter code refer to the sequence and structure of Dictyostelium myosin whereas those labeled with the single letter code for the amino acid residues refer to chicken skeletal myosin. This figure was prepared with the molecular graphics program MOLSCRIPT [Kraulis 1991].
Figure 7.
Figure 7. Stereo view of representative electron density associated with the central 50 kDa section of the polypeptide chain located near the fluorescent mant ring and calculated with coefficients of the form 2F[o]−F[c]. This Figure was prepared with the graphics programs MOLDED [Fisher 1996] and MOLSCRIPT [Kraulis 1991].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 274, 394-407) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21315083 D.J.Jacobs, D.Trivedi, C.David, and C.M.Yengo (2011).
Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle.
  J Mol Biol, 407, 716-730.  
21212073 K.Tanaka, T.Kimura, and S.Maruta (2011).
Synthesis of a novel fluorescent non-nucleotide ATP analogue and its interaction with myosin ATPase.
  J Biochem, 149, 395-403.  
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.  
18211892 M.Gyimesi, B.Kintses, A.Bodor, A.Perczel, S.Fischer, C.R.Bagshaw, and A.Málnási-Csizmadia (2008).
The mechanism of the reverse recovery step, phosphate release, and actin activation of Dictyostelium myosin II.
  J Biol Chem, 283, 8153-8163.  
17496049 D.I.García, P.Lanigan, M.Webb, T.G.West, J.Requejo-Isidro, E.Auksorius, C.Dunsby, M.Neil, P.French, and M.A.Ferenczi (2007).
Fluorescence lifetime imaging to detect actomyosin states in mammalian muscle sarcomeres.
  Biophys J, 93, 2091-2101.  
16377637 M.Sun, J.L.Oakes, S.K.Ananthanarayanan, K.H.Hawley, R.Y.Tsien, S.R.Adams, and C.M.Yengo (2006).
Dynamics of the upper 50-kDa domain of myosin V examined with fluorescence resonance energy transfer.
  J Biol Chem, 281, 5711-5717.  
15951390 C.I.Robertson, D.P.Gaffney, L.R.Chrin, and C.L.Berger (2005).
Structural rearrangements in the active site of smooth-muscle myosin.
  Biophys J, 89, 1882-1892.  
15647168 A.V.Somlyo, A.S.Khromov, M.R.Webb, M.A.Ferenczi, D.R.Trentham, Z.H.He, S.Sheng, Z.Shao, and A.P.Somlyo (2004).
Smooth muscle myosin: regulation and properties.
  Philos Trans R Soc Lond B Biol Sci, 359, 1921-1930.  
15647159 H.L.Sweeney, and A.Houdusse (2004).
The motor mechanism of myosin V: insights for muscle contraction.
  Philos Trans R Soc Lond B Biol Sci, 359, 1829-1841.  
15229653 R.Kagawa, M.G.Montgomery, K.Braig, A.G.Leslie, and J.E.Walker (2004).
The structure of bovine F1-ATPase inhibited by ADP and beryllium fluoride.
  EMBO J, 23, 2734-2744.
PDB codes: 1w0j 1w0k
15254035 S.S.Rosenfeld, and H.L.Sweeney (2004).
A model of myosin V processivity.
  J Biol Chem, 279, 40100-40111.  
12756255 K.Ito, T.Q.Uyeda, Y.Suzuki, K.Sutoh, and K.Yamamoto (2003).
Requirement of domain-domain interaction for conformational change and functional ATP hydrolysis in myosin.
  J Biol Chem, 278, 31049-31057.  
10617631 A.M.Gulick, C.B.Bauer, J.B.Thoden, E.Pate, R.G.Yount, and I.Rayment (2000).
X-ray structures of the Dictyostelium discoideum myosin motor domain with six non-nucleotide analogs.
  J Biol Chem, 275, 398-408.
PDB codes: 1d0x 1d0y 1d0z 1d1a 1d1b 1d1c
11123913 I.M.Li de La Sierra, J.Gallay, M.Vincent, T.Bertrand, P.Briozzo, O.Bârzu, and A.M.Gilles (2000).
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling.
  Biochemistry, 39, 15870-15878.  
10636874 J.M.Jault, S.Fieulaine, S.Nessler, P.Gonzalo, A.Di Pietro, J.Deutscher, and A.Galinier (2000).
The HPr kinase from Bacillus subtilis is a homo-oligomeric enzyme which exhibits strong positive cooperativity for nucleotide and fructose 1,6-bisphosphate binding.
  J Biol Chem, 275, 1773-1780.  
10827983 K.Oiwa, J.F.Eccleston, M.Anson, M.Kikumoto, C.T.Davis, G.P.Reid, M.A.Ferenczi, J.E.Corrie, A.Yamada, H.Nakayama, and D.R.Trentham (2000).
Comparative single-molecule and ensemble myosin enzymology: sulfoindocyanine ATP and ADP derivatives.
  Biophys J, 78, 3048-3071.  
10869438 S.N.Murthy, and L.Lorand (2000).
Nucleotide binding by the erythrocyte transglutaminase/Gh protein, probed with fluorescent analogs of GTP and GDP.
  Proc Natl Acad Sci U S A, 97, 7744-7747.  
  10493582 K.Kirshenbaum, M.Young, and S.Highsmith (1999).
Predicting allosteric switches in myosins.
  Protein Sci, 8, 1806-1815.  
10531338 P.G.Gillespie, S.K.Gillespie, J.A.Mercer, K.Shah, and K.M.Shokat (1999).
Engineering of the myosin-ibeta nucleotide-binding pocket to create selective sensitivity to N(6)-modified ADP analogs.
  J Biol Chem, 274, 31373-31381.  
9789020 C.M.Yengo, P.M.Fagnant, L.Chrin, A.S.Rovner, and C.L.Berger (1998).
Smooth muscle myosin mutants containing a single tryptophan reveal molecular interactions at the actin-binding interface.
  Proc Natl Acad Sci U S A, 95, 12944-12949.  
9578557 C.T.Murphy, and J.A.Spudich (1998).
Dictyostelium myosin 25-50K loop substitutions specifically affect ADP release rates.
  Biochemistry, 37, 6738-6744.  
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 codes are shown on the right.