3W34

Ternary complex of Thermus thermophilus HB8 uridine-cytidine kinase with substrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.209 

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This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Studies on the Reaction Mechanism of Uridine-Cytidine Kinase

Tomoike, F.Nakagawa, N.Kuramitsu, S.Masui, R.

(2015) Protein J 34: 411-420

  • DOI: 10.1007/s10930-015-9636-8
  • Primary Citation of Related Structures:  
    3W34

  • PubMed Abstract: 
  • Uridine-cytidine kinase catalyzes phosphorylation of the pyrimidine nucleosides uridine and cytidine and plays an important role in nucleotide metabolism. However, the detailed molecular mechanism of these reactions remains to be elucidated. Here, we determined the structure of the ternary complex of Uridine-cytidine kinase from Thermus thermophilus HB8 with both cytidine and β,γ-methyleneadenosine 5'-triphosphate, a non-hydrolysable ATP analogue ...

    Uridine-cytidine kinase catalyzes phosphorylation of the pyrimidine nucleosides uridine and cytidine and plays an important role in nucleotide metabolism. However, the detailed molecular mechanism of these reactions remains to be elucidated. Here, we determined the structure of the ternary complex of Uridine-cytidine kinase from Thermus thermophilus HB8 with both cytidine and β,γ-methyleneadenosine 5'-triphosphate, a non-hydrolysable ATP analogue. Substrate binding is accompanied by substantial domain movement that allows the substrate-binding cleft to close. The terminal phosphodiester bond of the ATP analogue is in an ideal location for an inline attack of the 5'-hydroxyl group of cytidine. Asp40 is located near the 5'-hydroxyl group of cytidine. Mutation of this conserved residue to Asn or Ala resulted in a complete loss of enzyme activity, which is consistent with the notion that Asp40 acts as a general base that activates the 5'-hydroxyl group of cytidine. The pH profile of the activity showed an apparent pK a value of 7.4. Based on this structure, a likely mechanism of the catalytic step is discussed.


    Organizational Affiliation

    Division of Biology and Geosciences, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan. rmasui@sci.osaka-cu.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uridine kinaseA, B211Thermus thermophilus HB8Mutation(s): 0 
Gene Names: udkTTHA0578
EC: 2.7.1.48
UniProt
Find proteins for Q5SKR5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKR5 
Go to UniProtKB:  Q5SKR5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACP (Subject of Investigation/LOI)
Query on ACP

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
CTN (Subject of Investigation/LOI)
Query on CTN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.73α = 90
b = 126.952β = 90
c = 61.726γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references