2IA5

T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase.

Zhu, H.Smith, P.Wang, L.K.Shuman, S.

(2007) Virology 366: 126-136

  • DOI: 10.1016/j.virol.2007.03.059
  • Primary Citation of Related Structures:  
    2IA5

  • PubMed Abstract: 
  • T4 polynucleotide kinase/phosphatase (Pnkp) exemplifies a family of bifunctional enzymes with 5'-kinase and 3' phosphatase activities that function in nucleic acid repair. T4 Pnkp is a homotetramer of a 301-aa polypeptide, which consists of an N-terminal kinase domain of the P-loop phosphotransferase superfamily and a C-terminal phosphatase domain of the DxD acylphosphatase superfamily ...

    T4 polynucleotide kinase/phosphatase (Pnkp) exemplifies a family of bifunctional enzymes with 5'-kinase and 3' phosphatase activities that function in nucleic acid repair. T4 Pnkp is a homotetramer of a 301-aa polypeptide, which consists of an N-terminal kinase domain of the P-loop phosphotransferase superfamily and a C-terminal phosphatase domain of the DxD acylphosphatase superfamily. The homotetramer is formed via pairs of phosphatase-phosphatase and kinase-kinase homodimer interfaces. Here we identify four side chains-Asp187, Ser211, Lys258, and Asp277-that are required for 3' phosphatase activity. Alanine mutations at these positions abolished phosphatase activity without affecting kinase function or tetramerization. Conservative substitutions of asparagine or glutamate for Asp187 did not revive the 3' phosphatase, nor did arginine or glutamine substitutions for Lys258. Threonine in lieu of Ser211 and glutamate in lieu of Asp277 restored full activity, whereas asparagine at position 277 had no salutary effect. We report a 3.0 A crystal structure of the Pnkp tetramer, in which a sulfate ion is coordinated between Arg246 and Arg279 in a position that we propose mimics one of the penultimate phosphodiesters (5'NpNpNp-3') of the polynucleotide 3'-PO(4) substrate. The amalgam of mutational and structural data engenders a plausible catalytic mechanism for the phosphatase that includes covalent catalysis (via Asp165), general acid-base catalysis (via Asp167), metal coordination (by Asp165, Asp277 and Asp278), and transition state stabilization (via Lys258, Ser211, backbone amides, and the divalent cation). Other critical side chains play architectural roles (Arg176, Asp187, Arg213, Asp254). To probe the role of oligomerization in phosphatase function, we introduced six double-alanine cluster mutations at the phosphatase-phosphatase domain interface, two of which (R297A-Q295A and E292A-D300A) converted Pnkp from a tetramer to a dimer and ablated phosphatase activity.


    Organizational Affiliation

    Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polynucleotide kinase
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
301Escherichia virus T4Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06855
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth I],
CA [auth D],
DA [auth D],
DB [auth J],
EA [auth D],
AB [auth I],
CA [auth D],
DA [auth D],
DB [auth J],
EA [auth D],
EB [auth J],
FB [auth J],
HA [auth E],
HB [auth K],
IA [auth E],
IB [auth K],
JA [auth E],
JB [auth K],
LA [auth F],
LB [auth L],
MA [auth F],
MB [auth L],
N [auth A],
NA [auth F],
NB [auth L],
O [auth A],
P [auth A],
PA [auth G],
QA [auth G],
RA [auth G],
S [auth B],
T [auth B],
U [auth B],
UA [auth H],
VA [auth H],
WA [auth H],
X [auth C],
Y [auth C],
YA [auth I],
Z [auth C],
ZA [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ARS
Query on ARS

Download Ideal Coordinates CCD File 
AA [auth C],
BB [auth I],
FA [auth D],
GB [auth J],
KA [auth E],
AA [auth C],
BB [auth I],
FA [auth D],
GB [auth J],
KA [auth E],
KB [auth K],
OA [auth F],
Q [auth A],
SA [auth G],
V [auth B],
XA [auth H]
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D],
CB [auth J],
GA [auth E],
M [auth A],
R [auth B],
BA [auth D],
CB [auth J],
GA [auth E],
M [auth A],
R [auth B],
TA [auth H],
W [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.63α = 90
b = 128.05β = 90
c = 357.12γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection