1KFV

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

PDB DOI: https://doi.org/10.2210/pdb1KFV/pdb
NAKB: 1KFV

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

Deposited: 2001-11-23 Released: 2002-06-14
Deposition Author(s): Serre, L., Pereira de Jesus, K., Boiteux, S., Zelwer, C., Castaing, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.285
R-Value Work: 0.251

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.

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

(2002) EMBO J 21: 2854-2865

PubMed: 12065399 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/emboj/cdf304
Primary Citation of Related Structures:
1KFV

PubMed Abstract:
The formamidopyrimidine-DNA glycosylase (Fpg, MutM) is a bifunctional base excision repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged DNA. The structure of a non-covalent complex between the Lactoccocus lactis Fpg and a 1,3-propanediol (Pr) abasic site analogue-containing DNA has been solved. Through an asymmetric interaction along the damaged strand and the intercalation of the triad (M75/R109/F111), Fpg pushes out the Pr site from the DNA double helix, recognizing the cytosine opposite the lesion and inducing a 60 degrees bend of the DNA. The specific recognition of this cytosine provides some structural basis for understanding the divergence between Fpg and its structural homologue endo nuclease VIII towards their substrate specificities. In addition, the modelling of the 8-oxoguanine residue allows us to define an enzyme pocket that may accommodate the extrahelical oxidized base.

Organizational Affiliation

Institut de Biologie Structurale, CNRS-CEA, 41 av. Jules Horowitz, 38027 Grenoble cedex 01, France.

Macromolecule Content

Total Structure Weight: 78.34 kDa
Atom Count: 5,345
Modelled Residue Count: 576
Deposited Residue Count: 594
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Formamido-pyrimidine DNA glycosylase	E [auth A], F [auth B]	271	Lactococcus lactis	Mutation(s): 5 Gene Names: MUTM or FPG 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42371
Sequence Annotations Expand
Reference Sequence

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPTPCPTPTPTP(PDI)PTPTPTPCPTP*C)-3'	A [auth D], C [auth G]	13	N/A
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(GPAPGPAPAPAPCPAPAPAPGPAP*G)-3'	B [auth E], D [auth H]	13	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B]	H [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.285
R-Value Work: 0.251
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.88	α = 90
b = 62.03	β = 104.7
c = 80.97	γ = 90

Software Package:

Software Name	Purpose
SnB	phasing
SOLVE	phasing
MOLREP	phasing
CNS	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-06-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-06-14
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2021-10-27
Changes: Database references, Derived calculations, Refinement description
Version 1.4: 2023-08-16
Changes: Data collection, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-10-30
Changes: Structure summary