2QQ0 | pdb_00002qq0

Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.217 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2QQ0

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes.

Segura-Pena, D.Lichter, J.Trani, M.Konrad, M.Lavie, A.Lutz, S.

(2007) Structure 15: 1555-1566

  • DOI: https://doi.org/10.1016/j.str.2007.09.025
  • Primary Citation Related Structures: 
    2QPO, 2QQ0, 2QQE

  • PubMed Abstract: 

    The human cytosolic thymidine kinase (TK) and structurally related TKs in prokaryotes play a crucial role in the synthesis and regulation of the cellular thymidine triphosphate pool. We report the crystal structures of the TK homotetramer from Thermotoga maritima in four different states: its apo-form, a binary complex with thymidine, as well as the ternary structures with the two substrates (thymidine/AppNHp) and the reaction products (TMP/ADP). In combination with fluorescence spectroscopy and mutagenesis experiments, our results demonstrate that ATP binding is linked to a substantial reorganization of the enzyme quaternary structure, leading to a transition from a closed, inactive conformation to an open, catalytic state. We hypothesize that these structural changes are relevant to enzyme function in situ as part of the catalytic cycle and serve an important role in regulating enzyme activity by amplifying the effects of feedback inhibitor binding.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, IL 60607, USA.

Macromolecule Content 

  • Total Structure Weight: 43.05 kDa 
  • Atom Count: 3,142 
  • Modeled Residue Count: 339 
  • Deposited Residue Count: 368 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thymidine kinase
A, B
184Thermotoga maritimaMutation(s): 0 
Gene Names: tdk
EC: 2.7.1.21
UniProt
Find proteins for Q9WYN2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYN2 
Go to UniProtKB:  Q9WYN2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYN2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
F [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
J [auth B]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
TMP

Query on TMP



Download:Ideal Coordinates CCD File
I [auth B]THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
THM

Query on THM



Download:Ideal Coordinates CCD File
E [auth A]THYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.16α = 90
b = 59.31β = 103.02
c = 61.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations