3LKM

1.6 Angstrom Crystal Structure of the Alpha-kinase Domain of Myosin Heavy Chain Kinase A Complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


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Literature

Crystal Structure of the {alpha}-Kinase Domain of Dictyostelium Myosin Heavy Chain Kinase A.

Ye, Q.Crawley, S.W.Yang, Y.Cote, G.P.Jia, Z.

(2010) Sci Signal 3: ra17-ra17

  • DOI: 10.1126/scisignal.2000525
  • Primary Citation of Related Structures:  
    3LKM, 3LLA, 3LMH, 3LMI

  • PubMed Abstract: 
  • Dictyostelium discoideum myosin II heavy chain kinase A (MHCK A) disrupts the assembly and cellular activity of bipolar filaments of myosin II by phosphorylating sites within its alpha-helical, coiled-coil tail. MHCK A is a member of the atypical alpha-kinase family of serine and threonine protein kinases and displays no sequence homology to typical eukaryotic protein kinases ...

    Dictyostelium discoideum myosin II heavy chain kinase A (MHCK A) disrupts the assembly and cellular activity of bipolar filaments of myosin II by phosphorylating sites within its alpha-helical, coiled-coil tail. MHCK A is a member of the atypical alpha-kinase family of serine and threonine protein kinases and displays no sequence homology to typical eukaryotic protein kinases. We report the crystal structure of the alpha-kinase domain (A-CAT) of MHCK A. When crystallized in the presence of adenosine triphosphate (ATP), A-CAT contained adenosine monophosphate (AMP) at the active site. However, when crystallized in the presence of ATP and a peptide substrate, which does not appear in the structure, adenosine diphosphate (ADP) was found at the active site and an invariant aspartic acid residue (Asp(766)) at the active site was phosphorylated. The aspartylphosphate group was exposed to the solvent within an active-site pocket that might function as a docking site for substrates. Access to the aspartylphosphate was regulated by a conformational switch in a loop that bound to a magnesium ion (Mg(2+)), providing a mechanism that allows alpha-kinases to sense and respond to local changes in Mg(2+).


    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myosin heavy chain kinase AA307Dictyostelium discoideumMutation(s): 0 
Gene Names: DDB_G0291231mhckAmhkA
EC: 2.7.11.7
UniProt
Find proteins for P42527 (Dictyostelium discoideum)
Explore P42527 
Go to UniProtKB:  P42527
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42527
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
H [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.224α = 90
b = 83.777β = 90
c = 44.364γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-03-16 
  • Deposition Author(s): Ye, Q., Jia, Z.

Revision History  (Full details and data files)

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