3W8R

Mutant structure of Thermus thermophilus HB8 uridine-cytidine kinase

• PDB DOI: https://doi.org/10.2210/pdb3W8R/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-03-21 Released: 2014-03-26 
• Deposition Author(s): Tomoike, F., Nakagawa, N., Masui, R., Kuramitsu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.283 
• R-Value Work: 0.221 

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

• PubMed: 28955773 
• DOI: https://doi.org/10.1016/j.bbrep.2017.07.002
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine kinase	A, B	211	Thermus thermophilus HB8	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	D [auth A], F [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
CTN	C [auth A], E [auth B]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C9 H13 N3 O5 UHDGCWIWMRVCDJ-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.283 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.3	α = 90
b = 124.1	β = 90
c = 60.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Tomoike, F., Nakagawa, N., Masui, R., Kuramitsu, S.

Revision History  

• 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