3JQ3

Crystal Structure of Lombricine Kinase, complexed with substrate ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The structure of lombricine kinase: implications for phosphagen kinase conformational changes.

Bush, D.J.Kirillova, O.Clark, S.A.Davulcu, O.Fabiola, F.Xie, Q.Somasundaram, T.Ellington, W.R.Chapman, M.S.

(2011) J Biol Chem 286: 9338-9350

  • DOI: 10.1074/jbc.M110.202796
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by ...

    Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.


    Related Citations: 
    • Cloning and expression of a lombricine kinase from an echiuroid worm: insights into structural correlates of substrate specificity
      Ellington, W.R., Bush, J.
      (2002) Biochem Biophys Res Commun 291: 939

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lombricine kinaseA366Urechis caupoMutation(s): 0 
EC: 2.7.3.5
Find proteins for Q8T6T7 (Urechis caupo)
Explore Q8T6T7 
Go to UniProtKB:  Q8T6T7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.692α = 90
b = 77.986β = 90
c = 141.122γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description