1LY1 | pdb_00001ly1

Structure and Mechanism of T4 Polynucleotide Kinase

• PDB DOI: https://doi.org/10.2210/pdb1LY1/pdb

• Classification: TRANSFERASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-06-06 Released: 2002-07-17 
• Deposition Author(s): Wang, L.K., Lima, C.D., Shuman, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.212 (DCC) 

Literature

Structure and mechanism of T4 polynucleotide kinase: an RNA repair enzyme.

Wang, L.K., Lima, C.D., Shuman, S.

(2002) EMBO J 21: 3873-3880

• PubMed: 12110598 
• DOI: https://doi.org/10.1093/emboj/cdf397
• Primary Citation Related Structures: 
  1LY1


• PubMed Abstract: 
  

  T4 polynucleotide kinase (Pnk), in addition to being an invaluable research tool, exemplifies a family of bifunctional enzymes with 5'-kinase and 3'-phosphatase activities that play key roles in RNA and DNA repair. T4 Pnk is a homotetramer composed of a C-terminal phosphatase domain and an N-terminal kinase domain. The 2.0 A crystal structure of the isolated kinase domain highlights a tunnel-like active site through the heart of the enzyme, with an entrance on the 5' OH acceptor side that can accommodate a single-stranded polynucleotide. The active site is composed of essential side chains that coordinate the beta phosphate of the NTP donor and the 3' phosphate of the 5' OH acceptor, plus a putative general acid that activates the 5' OH. The structure rationalizes the different specificities of T4 and eukaryotic Pnk and suggests a model for the assembly of the tetramer.

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Organizational Affiliation: 
• Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.06 kDa 
• Atom Count: 1,403 
• Modeled Residue Count: 152 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polynucleotide kinase	A	181	Tequatrovirus T4	Mutation(s): 0  Gene Names: PSET EC: 2.7.1.78 (PDB Primary Data), 3.1.3.34 (UniProt)
UniProt
Find proteins for P06855 (Enterobacteria phage T4) Explore P06855  Go to UniProtKB:  P06855

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.212 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.3	α = 90
b = 91.8	β = 90
c = 67.9	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-17 
Deposition Author(s): Wang, L.K., Lima, C.D., Shuman, S.

Revision History  

• Version 1.0: 2002-07-17
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations