1UKE

UMP/CMP KINASE FROM SLIME MOLD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 9716-9727

  • DOI: 10.1021/bi960642s
  • Also Cited By: 5UKD, 1QF9

  • PubMed Abstract: 
  • The three-dimensional structure of the UMP/CMP kinase (UK) from the slime mold Dictyostelium discoideum complexed with the specific and asymmetric bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) has been determined at a re ...

    The three-dimensional structure of the UMP/CMP kinase (UK) from the slime mold Dictyostelium discoideum complexed with the specific and asymmetric bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) has been determined at a resolution of 2.2 A. The structure of the enzyme, which has up to 41% sequence homology with known adenylate kinases (AK), represents a closed conformation with the flexible monophosphate binding domain (NMP site) being closed over the uridyl moiety of the dinucleotide. Two water molecules were found within hydrogen-bonding distance to the uracil base. The key residue for the positioning and stabilization of those water molecules appears to be asparagine 97, a residue that is highly specific for AK-homologous UMP kinases, but is almost invariably a glutamine in adenylate kinases. Other residues in this region are highly conserved among AK-related NMP kinases. The catalytic Mg2+ ion is coordinated with octahedral geometry to four water molecules and two oxygens of the phosphate chain of UP5A but has no direct interactions with the protein. The comparison of the geometry of the UKdicty.UP5A.Mg2+ complex with the previously reported structure of the UKyeast.ADP.ADP complex [Müller-Dieckmann & Schulz (1994) J. Mol. Biol. 236, 361-367] suggests that UP5A in our structure mimics an ADP.Mg.UDP biproduct inhibitor rather than an ATP. MG.UMP bisubstrate inhibitor.


    Related Citations: 
    • Substrate Specificity and Assembly of the Catalytic Center Derived from Two Structures of Ligated Uridylate Kinase
      Muller-Dieckmann, H.J.,Schulz, G.E.
      (1995) J.Mol.Biol. 246: 522
    • Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases
      Vonrhein, C.,Schlauderer, G.J.,Schulz, G.E.
      (1995) Structure 3: 483
    • 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
    • High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer
      Abele, U.,Schulz, G.E.
      (1995) Protein Sci. 4: 1262
    • 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 Medizinische Forschung, Abteilung Biophysik, Heidelberg, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UP5
Query on UP5

Download SDF File 
Download CCD File 
A
P1-(ADENOSINE-5'-P5-(URIDINE-5')PENTAPHOSPHATE
C19 H28 N7 O24 P5
CPTLFMDLEWCNMJ-KPKSGTNCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.500α = 90.00
b = 78.500β = 90.00
c = 101.500γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance