2UKD | pdb_00002ukd

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

• PDB DOI: https://doi.org/10.2210/pdb2UKD/pdb

• Classification: TRANSFERASE
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-05-20 Released: 1998-05-20 
• Deposition Author(s): Schlichting, I., Reinstein, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.231 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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

• PubMed: 9280438 
• DOI: https://doi.org/10.1021/bi970974c
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.75 kDa 
• Atom Count: 1,697 
• Modeled Residue Count: 191 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE	A	194	Dictyostelium discoideum	Mutation(s): 0  Gene Names: KCY_DICDI EC: 2.7.4.14
UniProt
Find proteins for P20425 (Dictyostelium discoideum) Explore P20425  Go to UniProtKB:  P20425

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
C5P	D [auth A]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.231 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 78.7	β = 90
c = 100.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-20 
Deposition Author(s): Schlichting, I., Reinstein, J.

Revision History  

• 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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Other