1LTQ | pdb_00001ltq

CRYSTAL STRUCTURE OF T4 POLYNUCLEOTIDE KINASE

• PDB DOI: https://doi.org/10.2210/pdb1LTQ/pdb

• Classification: TRANSFERASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-05-20 Released: 2002-10-09 
• Deposition Author(s): Galburt, E.A., Pelletier, J., Wilson, G., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.261 (Depositor) 
• R-Value Work: 
  0.236 (Depositor) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.

Galburt, E.A., Pelletier, J., Wilson, G., Stoddard, B.L.

(2002) Structure 10: 1249-1260

• PubMed: 12220496 
• DOI: https://doi.org/10.1016/s0969-2126(02)00835-3
• Primary Citation Related Structures: 
  1LTQ


• PubMed Abstract: 
  

  T4 phage polynucleotide kinase (PNK) was identified over 35 years ago and has become a staple reagent for molecular biologists. The enzyme displays 5'-hydroxyl kinase, 3'-phosphatase, and 2',3'-cyclic phosphodiesterase activities against a wide range of substrates. These activities modify the ends of nicked tRNA generated by a bacterial response to infection and facilitate repair by T4 RNA ligase. DNA repair enzymes that share conserved motifs with PNK have been identified in eukaryotes. PNK contains two functionally distinct structural domains and forms a homotetramer. The C-terminal phosphatase domain is homologous to the L-2-haloacid dehalogenase family and the N-terminal kinase domain is homologous to adenylate kinase. The active sites have been characterized through structural homology analyses and visualization of bound substrate.

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Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center and The Graduate Program in Biomolecular Structure and Design, University of Washington, 1100 Fairview Avenue North, A3-023, Seattle, WA 98109, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.74 kDa 
• Atom Count: 2,532 
• Modeled Residue Count: 298 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYNUCLEOTIDE KINASE	A	301	Tequatrovirus T4	Mutation(s): 12  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.261 (Depositor) 
• R-Value Work:  0.236 (Depositor) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.585	α = 90
b = 93.684	β = 90
c = 124.165	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-09 
Deposition Author(s): Galburt, E.A., Pelletier, J., Wilson, G., Stoddard, B.L.

Revision History  

• Version 1.0: 2002-10-09
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary