1K3X

Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.

Zharkov, D.O.Golan, G.Gilboa, R.Fernandes, A.S.Gerchman, S.E.Kycia, J.H.Rieger, R.A.Grollman, A.P.Shoham, G.

(2002) EMBO J. 21: 789-800

  • DOI: 10.1093/emboj/21.4.789
  • Primary Citation of Related Structures:  1K3W

  • PubMed Abstract: 
  • Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal ...

    Endonuclease VIII (Nei) of Escherichia coli is a DNA repair enzyme that excises oxidized pyrimidines from DNA. Nei shares with formamidopyrimidine-DNA glycosylase (Fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. However, Nei differs significantly from Fpg in substrate specificity. We determined the structure of Nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 A resolution. The crosslink is derived from a Schiff base intermediate that precedes beta-elimination and is stabilized by reduction with NaBH(4). Nei consists of two domains connected by a hinge region, creating a DNA binding cleft between domains. DNA in the complex is sharply kinked, the deoxyribitol moiety is bound covalently to Pro1 and everted from the duplex into the active site. Amino acids involved in substrate binding and catalysis are identified. Molecular modeling and analysis of amino acid conservation suggest a site for recognition of the damaged base. Based on structural features of the complex and site-directed mutagenesis studies, we propose a catalytic mechanism for Nei.


    Organizational Affiliation

    Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Endonuclease VIII
A
262Escherichia coli (strain K12)Gene Names: nei
EC: 3.2.2.-, 4.2.99.18
Find proteins for P50465 (Escherichia coli (strain K12))
Go to UniProtKB:  P50465
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3'B13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'C13N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PED
Query on PED
C
NON-POLYMERC5 H13 O6 P

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BRU
Query on BRU
B
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.495α = 90.00
b = 76.495β = 90.00
c = 164.310γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SHELXphasing
DENZOdata reduction
SHELXmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance