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Overview for MACiE Entry M0162

Version history

General Information

EC Number: 3.1.25.1 (A member of the Hydrolases, Acting on ester bonds, Site-specific endodeoxyribonucleases that are specific for altered bases)

Enzyme Name: deoxyribonuclease (pyrimidine dimer)

Biological Species: Bacteriophage t4 (Virus)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1vas - ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIRENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASISFOR DAMAGED DNA RECOGNITION (Resolution = 2.75 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of cyclobutane pyrimidine dimer

Image of water

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Image of cyclobutane pyrimidine dimer 5'-phosphate

Image of DNA 3'-a,b-unsaturated aldehyde

cyclobutane pyrimidine dimer
X00066
water
C00001
CHEBI:15377
cyclobutane pyrimidine dimer 5'-phosphate
X00067
DNA 3'-a,b-unsaturated aldehyde
X00068

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Stepwise Description of the Reaction

Step 1The N-terminus of the enzyme, Thr2, attacks the C1 carbon of the deoxyribose ring at the 5' end of the DNA molecule in a nucleophilic substitution, cleaving the bond to the damaged base
Step 2The oxyanion initiates an isomerisation which causes the nitrogen of the base to deprotonate water, which in turn deprotonates the N-terminal Thr2.
Step 3The lone pair on the N-terminal Thr2 initiates an elimination, cleaving the C1-O bond of the deoxyribose ring, which in turn deprotonates Glu23
Step 4Glu23 deprotonates the C2 of the deoxyribose ring, causing a double bond rearrangement.
Step 5The lone pair on the N-terminal Thr2 initiates an elimination of the phosphate, which in turn deprotonates Glu23
Step 6Glu23 deprotonates water, which attacks the C1 bound to the N-terminal Thr2 in a nucleophilic addition.
Step 7The N-terminal Thr2 deprotonates the newly formed alcohol group.
Step 8The oxyanion initiates an elimination of the N-terminal Thr2, regenerating the enzyme active site.

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Catalytic Residues Involved

Type Number Chain Location of Function
Thr 2 A Main Chain N Terminus
Arg 22 A Side Chain
Glu 23 A Side Chain
Arg 26 A Side Chain

References

  1. D. G. Vassylyev et al. (1995), Cell, 83, 773-782. Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
    Medline: 8521494
  2. M. Fuxreiter et al. (1999), Biochemistry, 38, 9577-9589. Role of active site residues in the glycosylase step of T4 endonuclease V. Computer simulation studies on ionization states.
    Medline: 10423235

Homologue information for M0162 (1vas)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

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nuclease activity (molecular function)
endonuclease activity (molecular function)
DNA repair (biological process)
cellular response to DNA damage stimulus (biological process)
metabolic process (biological process)
hydrolase activity (molecular function)
hydrolase activity, acting on glycosyl bonds (molecular function)
deoxyribonuclease (pyrimidine dimer) activity (molecular function)
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