Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.16 kDa 
• Atom Count: 3170 
• Modelled Residue Count: 344 
• Deposited Residue Count: 368 
• Unique protein chains: 1

2ORW

Thermotoga maritima thymidine kinase 1 like enzyme in complex with TP4A

• PDB DOI: 10.2210/pdb2ORW/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-04 Released: 2007-03-27 
• Deposition Author(s): Segura-Pena, D., Lutz, S., Monnerjahn, C., Konrad, M., Lavie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.208 
• R-Value Work: 0.169 
• R-Value Observed: 0.173 

Literature

Binding of ATP to TK1-like Enzymes Is Associated with a Conformational Change in the Quaternary Structure.

Segura-Pena, D., Lutz, S., Monnerjahn, C., Konrad, M., Lavie, A.

(2007) J Mol Biol 369: 129-141

• PubMed: 17407781 
• DOI: 10.1016/j.jmb.2007.02.104
• Primary Citation of Related Structures:  
  2ORV, 2ORW


• PubMed Abstract: 
  

Human thymidine kinase 1 (hTK1) and structurally related TKs from other organisms catalyze the initial phosphorylation step in the thymidine salvage pathway. Though ATP is known to be the preferred phosphoryl donor for TK1-like enzymes, its exact binding mode and effect on the oligomeric state has not been analyzed. Here we report the structures of hTK1 and of the Thermotoga maritima thymidine kinase (TmTK) in complex with the bisubstrate inhibitor TP4A. The TmTK-TP4A structure reveals that the adenosine moiety of ATP binds at the subunit interface of the homotetrameric enzyme and that the majority of the ATP-enzyme interactions occur between the phosphate groups and the P-loop. In the hTK1 structure the adenosine group of TP4A exhibited no electron density. This difference between hTK1 and TmTK is rationalized by a difference in the conformation of their quaternary structure. A more open conformation, as seen in the TmTK-TP4A complex structure, is required to provide space for the adenosine moiety. Our analysis supports the formation of an analogous open conformation in hTK1 upon ATP binding.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A, B	184	Thermotoga maritima	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4TA	G [auth B], H [auth B]	P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE C20 H25 N7 O20 P4 WLGHSSFVEUABFP-SLFMBYJQSA-J
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.208 
• R-Value Work: 0.169 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.55	α = 90
b = 59.63	β = 103.11
c = 61.44	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-04 
• Released Date: 2007-03-27 
Deposition Author(s): Segura-Pena, D., Lutz, S., Monnerjahn, C., Konrad, M., Lavie, A.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance