3UKD

UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, CMP, AND ALF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.

Schlichting, I.Reinstein, J.

(1997) Biochemistry 36: 9290-9296

  • DOI: https://doi.org/10.1021/bi970974c
  • Primary Citation of Related Structures:  
    2UKD, 3UKD, 4UKD

  • PubMed Abstract: 

    UMP/CMP kinase from Dictyostelium discoideum (UmpKdicty) catalyzes the specific transfer of the terminal phosphate of ATP to UMP or CMP. Crystal structures of UmpKdicty with substrates and the transition state analogs AlF3 or BeF2 that lock UmpKdicty in active conformations were solved. The positions of the catalytic Mg2+ and the highly conserved lysine of the P loop are virtually invariant in the different structures. In contrast, catalytic arginines move to stabilize charges that develop during this reaction. The location of the arginines indicates formation of negative charges during the reaction at the transferred phosphoryl group, but not at the phosphate bridging oxygen atoms. This is consistent with an associative phosphoryl transfer mechanism but not with a dissociative one.


  • Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung physikalische Biochemie, Rheinlanddamm 201, D-44139 Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE194Dictyostelium discoideumMutation(s): 0 
Gene Names: KCY_DICDI
EC: 2.7.4.14
UniProt
Find proteins for P20425 (Dictyostelium discoideum)
Explore P20425 
Go to UniProtKB:  P20425
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20425
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.8α = 90
b = 78.8β = 90
c = 100.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-20
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Other