3M10

Substrate-free form of Arginine Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.727 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility.

Niu, X.Bruschweiler-Li, L.Davulcu, O.Skalicky, J.J.Bruschweiler, R.Chapman, M.S.

(2011) J.Mol.Biol. 405: 479-496

  • DOI: 10.1016/j.jmb.2010.11.007

  • PubMed Abstract: 
  • The phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a "high-energy" phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced ...

    The phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a "high-energy" phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of AK structures were interpreted as a plastic deformation. Here, the structure of Limulus substrate-free AK is refined against high-resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa) and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.7 Å transition-state analog complex shows large substrate-induced domain motions that can be broken down into movements of smaller quasi-rigid bodies. The solution-state structure of substrate-free AK is most consistent with an equilibrium of substrate-free and substrate-bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, "substrate-induced" motions are along modes that are intrinsically flexible in the substrate-free enzyme and likely involve some degree of conformational selection.


    Related Citations: 
    • Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase.
      Yousef, M.S.,Clark, S.A.,Pruett, P.K.,Somasundaram, T.,Ellington, W.R.,Chapman, M.S.
      (2003) Protein Sci. 12: 103
    • De-icing: recovery of diffraction intensities in the presence of ice rings.
      Chapman, M.S.,Somasundaram, T.
      (2010) Acta Crystallogr.,Sect.D 66: 741


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginine kinase
A, B
357Limulus polyphemusEC: 2.7.3.3
Find proteins for P51541 (Limulus polyphemus)
Go to UniProtKB:  P51541
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.727 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.218α = 90.00
b = 90.428β = 111.02
c = 70.554γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
Deice.pydata reduction
CNSrefinement
ADSCdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance