1NNJ

Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing DNA

• PDB DOI:  https://doi.org/10.2210/pdb1NNJ/pdb
• NAKB: 1NNJ

• Classification: HYDROLASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-14 Released: 2003-02-11 
• Deposition Author(s): Serre, L., Pereira de Jesus, K., Boiteux, S., Zelwer, C., Castaing, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.215 

Literature

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA.

Pereira de Jesus, K., Serre, L., Zelwer, C., Castaing, B.

(2005) Nucleic Acids Res 33: 5936-5944

• PubMed: 16243784 
• DOI: https://doi.org/10.1093/nar/gki879
• Primary Citation of Related Structures:  
  1NNJ, 1PJI, 1PJJ, 1PM5


• PubMed Abstract: 
  

Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3' and 5' sides by betadelta-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5'-C4'-C3' diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4' leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.

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Related Citations: 

• Crystallization and primary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA
  Pereira de Jesus, K., Serre, L., Hervouet, N., Bouckson-Castaing, V., Zelwer, C., Castaing, B.
  (2002) Acta Crystallogr D Biol Crystallogr 58: 679

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Organizational Affiliation: 

Centre de Biophysique Moléculaire, CNRS rue Charles Sadron, 45071 Orléans cedex 02, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.69 kDa 
• Atom Count: 2,973 
• Modelled Residue Count: 295 
• Deposited Residue Count: 299 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Formamidopyrimidine-DNA glycosylase	C [auth A]	271	Lactococcus lactis	Mutation(s): 1  Gene Names: mutM EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for P42371 (Lactococcus lactis subsp. cremoris) Explore P42371  Go to UniProtKB:  P42371

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3'	A [auth D]	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'	B [auth E]	14	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D, F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1NNJ	Kd: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.215 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.15	α = 90
b = 92.15	β = 90
c = 142.53	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-11 
Deposition Author(s): Serre, L., Pereira de Jesus, K., Boiteux, S., Zelwer, C., Castaing, B.

Revision History  

• Version 1.0: 2003-02-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations