4PPX | pdb_00004ppx

DNA Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position

• PDB DOI: https://doi.org/10.2210/pdb4PPX/pdb
• NAKB: 4PPX

• Classification: TRANSFERASE, LYASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-02-27 Released: 2014-04-02 
• Deposition Author(s): Eckenroth, B.E., Doublie, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of DNA Polymerase beta with DNA Containing the Base Lesion Spiroiminodihydantoin in a Templating Position.

Eckenroth, B.E., Fleming, A.M., Sweasy, J.B., Burrows, C.J., Doublie, S.

(2014) Biochemistry 53: 2075-2077

• PubMed: 24649945 
• DOI: https://doi.org/10.1021/bi500270e
• Primary Citation Related Structures: 
  4PPX


• PubMed Abstract: 
  

  The first high-resolution crystal structure of spiroiminodihydantoin (dSp1) was obtained in the context of the DNA polymerase β active site and reveals two areas of significance. First, the structure verifies the recently determined S configuration at the spirocyclic carbon. Second, the distortion of the DNA duplex is similar to that of the single-oxidation product 8-oxoguanine. For both oxidized lesions, adaptation of the syn conformation results in similar backbone distortions in the DNA duplex. The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove.

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Organizational Affiliation: 
• Department of Microbiology and Molecular Genetics, University of Vermont , Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 47.79 kDa 
• Atom Count: 3,452 
• Modeled Residue Count: 345 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	335	Homo sapiens	Mutation(s): 1  Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746  Go to UniProtKB:  P06746
PHAROS:  P06746 GTEx:  ENSG00000070501

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*AP*CP*(SDH)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'	B [auth T]	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'	C [auth P]	10	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*GP*G)-3'	D	5	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.276	α = 90
b = 79.102	β = 105.4
c = 54.742	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Eckenroth, B.E., Doublie, S.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-04-23
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description