3UKD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/bi970974c
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Related Citations: 
    • Crystal Structure of the Complex of Ump/Cmp Kinase from Dictyostelium Discoideum and the Bisubstrate Inhibitor P1-(5'-Adenosyl) P5-(5'-Uridyl) Pentaphosphate (Up5A) and Mg2+ at 2.2 A: Implications for Water-Mediated Specificity
      Scheffzek, K.,Kliche, W.,Wiesmuller, L.,Reinstein, J.
      (1996) Biochemistry 35: 9716
    • Cdna-Derived Sequence of Ump-Cmp Kinase from Dictyostelium Discoideum and Expression of the Enzyme in Escherichia Coli
      Wiesmuller, L.,Noegel, A.A.,Barzu, O.,Gerisch, G.,Schleicher, M.
      (1990) J.Biol.Chem. 265: 6339
    • Crystallization and Preliminary X-Ray Analysis of Ump/Cmp-Kinase from Dictyostelium Discoideum with the Specific Bisubstrate Inhibitor P1-(Adenosine 5')-P5-(Uridine 5')-Pentaphosphate (Up5A)
      Wiesmuller, L.,Scheffzek, K.,Kliche, W.,Goody, R.S.,Wittinghofer, A.,Reinstein, J.
      (1995) FEBS Lett. 363: 22


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE
A
194Dictyostelium discoideumMutation(s): 0 
Gene Names: pyrK (ctpS)
EC: 2.7.4.14
Find proteins for P20425 (Dictyostelium discoideum)
Go to UniProtKB:  P20425
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
C5P
Query on C5P

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
A
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.800α = 90.00
b = 78.800β = 90.00
c = 100.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-20
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance