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 1.2 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:  
    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 ...

    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
    • 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
    • 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

    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
MoleculeChainsSequence LengthOrganismDetailsImage
URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASEA194Dictyostelium discoideumMutation(s): 0 
Gene Names: KCY_DICDIpyrKctpSDDB_G0287495
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
C5P
Query on C5P

Download Ideal Coordinates CCD File 
D [auth A]CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
AF3
Query on AF3

Download Ideal Coordinates CCD File 
E [auth A]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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