1RC8 | pdb_00001rc8

T4 Polynucleotide Kinase bound to 5'-GTCAC-3' ssDNA

PDB DOI: https://doi.org/10.2210/pdb1RC8/pdb
NAKB: 1RC8

Classification: TRANSFERASE/DNA
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2003-11-03 Released: 2004-02-17
Deposition Author(s): Eastberg, J.H., Pelletier, J., Stoddard, B.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.294 (Depositor), 0.293 (DCC)
R-Value Work:
0.230 (Depositor), 0.231 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.

Eastberg, J.H., Pelletier, J., Stoddard, B.L.

(2004) Nucleic Acids Res 32: 653-660

PubMed: 14754987 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkh212
Primary Citation Related Structures:
1RC8, 1RPZ, 1RRC

PubMed Abstract:
T4 phage polynucleotide kinase (PNK) displays 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. The enzyme phosphorylates the 5' hydroxyl termini of a wide variety of nucleic acid substrates, a behavior studied here through the determination of a series of crystal structures with single-stranded (ss)DNA oligonucleotide substrates of various lengths and sequences. In these structures, the 5' ribose hydroxyl is buried in the kinase active site in proper alignment for phosphoryl transfer. Depending on the ssDNA length, the first two or three nucleotide bases are well ordered. Numerous contacts are made both to the phosphoribosyl backbone and to the ordered bases. The position, side chain contacts and internucleotide stacking interactions of the ordered bases are strikingly different for a 5'-GT DNA end than for a 5'-TG end. The base preferences displayed at those positions by PNK are attributable to differences in the enzyme binding interactions and in the DNA conformation for each unique substrate molecule.

Organizational Affiliation

Fred Hutchinson Cancer Research Center and the Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98109, USA.

Macromolecule Content

Total Structure Weight: 37.26 kDa
Atom Count: 2,436
Modeled Residue Count: 292
Deposited Residue Count: 306
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polynucleotide kinase	B [auth A]	301	Tequatrovirus T4	Mutation(s): 12 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06855
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(GPTPCPAP*C)-3'	A [auth B]	5	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.294 (Depositor), 0.293 (DCC)
R-Value Work: 0.230 (Depositor), 0.231 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.17	α = 90
b = 92.061	β = 90
c = 123.385	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2004-02-17

Deposition Author(s):

Eastberg, J.H.

Pelletier, J.

Stoddard, B.L.

Revision History (Full details and data files)

Version 1.0: 2004-02-17
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-11-13
Changes: Structure summary