3W8R | pdb_00003w8r

Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.283 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.220 (DCC) 

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This is version 1.3 of the entry. See complete history. 

Literature

Indispensable residue for uridine binding in the uridine-cytidine kinase family.

Tomoike, F., Nakagawa, N., Fukui, K., Yano, T., Kuramitsu, S., Masui, R.

(2017) Biochem Biophys Rep 11: 93-98

  • DOI: https://doi.org/10.1016/j.bbrep.2017.07.002
  • Primary Citation Related Structures: 
    3W8R

  • PubMed Abstract: 

    Uridine-cytidine kinase (UCK), including human UCK2, are a family of enzymes that generally phosphorylate both uridine and cytidine. However, UCK of Thermus thermophilus HB8 (ttCK) phosphorylates only cytidine. This cytidine-restricted activity is thought to depend on Tyr93, although the precise mechanism remains unresolved. Exhaustive mutagenesis of Tyr93 in ttCK revealed that the uridine phosphorylation activity was restored only by replacement of Tyr93 with His or Gln. Replacement of His117 in human UCK2, corresponding to residue Tyr93 in ttCK, by Tyr resulted in a loss of uridine phosphorylation activity. These findings indicated that uridine phosphorylation activity commonly depends on a single residue in the UCK family.

    • Organizational Affiliation: 
    • Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content 

  • Total Structure Weight: 48.87 kDa 
  • Atom Count: 3,366 
  • Modeled Residue Count: 413 
  • Deposited Residue Count: 422 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uridine kinase
A, B
211Thermus thermophilus HB8Mutation(s): 1 
Gene Names: TTHA0578, udk
EC: 2.7.1.48
UniProt
Find proteins for Q5SKR5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKR5 
Go to UniProtKB:  Q5SKR5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKR5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.283 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.3α = 90
b = 124.1β = 90
c = 60.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Advisory, Database references, Refinement description
  • Version 1.2: 2019-12-25
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Advisory, Data collection, Database references, Derived calculations