S00016
type: Enzyme
cath: Endonuclease V
ec: https://purl.uniprot.org/enzyme/3.1.25.1
csa: 1vas
macie: M0162
uniprot: P04418
kegg enzyme: deoxyribonuclease (pyrimidine dimer)
kegg enzyme: endodeoxyribonuclease (pyrimidine dimer)
kegg enzyme: bacteriophage T4 endodeoxyribonuclease V
kegg enzyme: T4 endonuclease V
kegg substrate: cys-syn pyrimidine dimer in DNA
kegg substrate: H2O
kegg product: DNA 5'-phosphate
kegg product: DNA 3'-trans-alpha,beta unsaturated aldehyde
pdb: 1endA
pdb: 1eniA
pdb: 1enjA
pdb: 1enkA
pdb: 1vasA
pdb: 2endA
pdb bound state: Unbound
  compound: cys-syn pyrimidine dimer in DNA
  pdb: 1endA
pdb bound state: Unbound
  compound: cys-syn pyrimidine dimer in DNA
  pdb: 1eniA
pdb bound state: Unbound
  compound: cys-syn pyrimidine dimer in DNA
  pdb: 1enjA
pdb bound state: Unbound
  compound: cys-syn pyrimidine dimer in DNA
  pdb: 1enkA
pdb bound state: Unbound
  compound: cys-syn pyrimidine dimer in DNA
  pdb: 2endA
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1endA
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1eniA
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1enjA
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1enkA
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 1vasA
pdb bound state: Unbound
  compound: DNA 5'-phosphate
  pdb: 2endA
pdb bound state: Unbound
  compound: DNA 3'-trans-alpha,beta unsaturated aldehyde
  pdb: 1endA
pdb bound state: Unbound
  compound: DNA 3'-trans-alpha,beta unsaturated aldehyde
  pdb: 1eniA
pdb bound state: Unbound
  compound: DNA 3'-trans-alpha,beta unsaturated aldehyde
  pdb: 1enjA
pdb bound state: Unbound
  compound: DNA 3'-trans-alpha,beta unsaturated aldehyde
  pdb: 1enkA
pdb bound state: Unbound
  compound: DNA 3'-trans-alpha,beta unsaturated aldehyde
  pdb: 1vasA
pdb bound state: Unbound
  compound: DNA 3'-trans-alpha,beta unsaturated aldehyde
  pdb: 2endA
active site residues resources: Structural determinants for specific recognition by T4 endonuclease V.
active site residues resources: P04418
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 2
  reference section: Fig. 1, p.51-54
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 6
  reference section: Scheme 1, p.17637-17638
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 9
  reference section: Fig.1
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 10
  reference section: Fig.1, p.9424
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 11
  reference section: p.524-525
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 12
  reference section: Fig.1
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 14
  reference section: Fig.8, p.182-193
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 15
  reference section: Fig.1, p.201-205
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 17
  reference section: Fig.1
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 18
  reference section: Fig.4, p.778-779
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 19
  reference section: Fig.1, p.2660-2661
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 20
  reference section: p.369-371
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 21
references: Preliminary crystallographic study of pyrimidine dimer-specific excision-repair enzyme from bacteriophage T4.
references: Structure-function studies of the T4 endonuclease V repair enzyme.
references: Site-directed mutagenesis of the T4 endonuclease V gene: mutations which enhance enzyme specific activity at low salt concentrations.
references: Mutations in endonuclease V that affect both protein-protein association and target site location.
references: Selective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding.
references: Reductive methylation of the amino terminus of endonuclease V eradicates catalytic activities. Evidence for an essential role of the amino terminus in the chemical mechanisms of catalysis.
references: Site-directed deletion mutagenesis within the T4 endonuclease V gene: dispensable sequences within putative loop regions.
references: Atomic structure of a pyrimidine-dimer specific excision-repair enzyme from bacteriophage T4.
references: Participation of glutamic acid 23 of T4 endonuclease V in the beta-elimination reaction of an abasic site in a synthetic duplex DNA.
references: Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V.
references: X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer.
references: Evidence for an imino intermediate in the T4 endonuclease V reaction.
references: Structure/function analysis of the Ala116-->Lys121 region of endonuclease V by random targeted mutagenesis.
references: T4 endonuclease V. Perspectives on catalysis.
references: Crystal structure of T4 endonuclease V. An excision repair enzyme for a pyrimidine dimer.
references: Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA.
references: Reaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes.
references: Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
references: Involvement of glutamic acid 23 in the catalytic mechanism of T4 endonuclease V.
references: Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.
references: Structural determinants for specific recognition by T4 endonuclease V.
references: Role of specific amino acid residues in T4 endonuclease V that alter nontarget DNA binding.
references: The role of base flipping in damage recognition and catalysis by T4 endonuclease V.
references: Characterization of a novel cis-syn and trans-syn-II pyrimidine dimer glycosylase/AP lyase from a eukaryotic algal virus, Paramecium bursaria chlorella virus-1.
references: Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.
references: Processivity of DNA repair enzymes.
references: Interaction of T4 endonuclease V with DNA: importance of the flexible loop regions in protein-DNA interaction.
comment: Although this enzyme classified into hydrolase (E.C. 3.-.-.-), it does not catalyzes hydrolysis. According to the literature [18], [19], [20], [23] & [25], this enzyme catalyzes the following reactions succesively, although the detailed mechanism has not been elucidated. (I) glycosylase reaction to form Schiff-base intermediate. (A) Transfer of deoxyribose group from pyrimidine dimer to the N-terminal alpha-amino group. (B) Eliminative double-bond formation; Ring opening of deoxyribose, forming Schiff-base intermediate. (II) AP lyase reaction. (C) Isomerization; Shift of double-bond from Schiff-base to adjacent bond. (D) Eliminative double-bond formation; beta-elimination of 3'-phosphate from the opened deoxyribose group. (E) Exchange of double-bonded atoms; Schiff-base deformation (hydration) #### The N-terminal alpha-amino group of Thr2 forms Schiff-base with C1' atom of the deoxyribose. Glu23 seems to be required for both reactions, (I) & (II).

Endonuclease V
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/1.10.440.10
catalytic domain: index.html

cys-syn pyrimidine dimer in DNA
type: KeggSubstrate
references: KEGG:L00011
compound type: nucleic acids

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

DNA 5'-phosphate
type: KeggProduct
references: KEGG:C00578
compound type: nucleic acids
compound type: phosphate group/phosphate ion

DNA 3'-trans-alpha,beta unsaturated aldehyde
type: KeggProduct
references: KEGG:L00013
compound type: nucleic acids
compound type: carbohydrate

1endA
type: Pdb
references: 1end
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1end
catalytic residue: GLU 23;ARG 26
main chain in catalysis: THR 2

1eniA
type: Pdb
references: 1eni
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1eni
catalytic residue: GLU 23;ARG 26
main chain in catalysis: THR 2

1enjA
type: Pdb
references: 1enj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1enj
catalytic residue: ;ARG 26
main chain in catalysis: THR 2
comment: mutant E23Q

1enkA
type: Pdb
references: 1enk
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1enk
catalytic residue: ;ARG 26
main chain in catalysis: THR 2
comment: mutant E23D

1vasA
type: Pdb
references: 1vas
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1vas
catalytic residue: ;ARG 26
main chain in catalysis: THR 2
comment: mutant E23Q

2endA
type: Pdb
references: 2end
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2end
catalytic residue: GLU 23;ARG 26
main chain in catalysis: THR 2

Preliminary crystallographic study of pyrimidine dimer-specific excision-repair enzyme from bacteriophage T4.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/3172233
journal: J Mol Biol
volume: 202
pages: 683-4
published year: 1988
authors:
  item: Morikawa K
  item: Tsujimoto M
  item: Ikehara M
  item: Inaoka T
  item: Ohtsuka E

Structure-function studies of the T4 endonuclease V repair enzyme.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2671706
journal: Mutat Res
volume: 218
pages: 49-65
published year: 1989
authors:
  item: Dodson ML
  item: Lloyd RS

Site-directed mutagenesis of the T4 endonuclease V gene: mutations which enhance enzyme specific activity at low salt concentrations.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2695926
journal: Proteins
volume: 6
pages: 128-38
published year: 1989
authors:
  item: Lloyd RS
  item: Augustine ML

Mutations in endonuclease V that affect both protein-protein association and target site location.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1888726
journal: Biochemistry
volume: 30
pages: 8638-48
published year: 1991
authors:
  item: Nickell C
  item: Lloyd RS

Selective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2037608
journal: J Biol Chem
volume: 266
pages: 10686-93
published year: 1991
authors:
  item: Prince MA
  item: Friedman B
  item: Gruskin EA
  item: Schrock RD 3rd
  item: Lloyd RS

Reductive methylation of the amino terminus of endonuclease V eradicates catalytic activities. Evidence for an essential role of the amino terminus in the chemical mechanisms of catalysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1894643
journal: J Biol Chem
volume: 266
pages: 17631-9
published year: 1991
authors:
  item: Schrock RD 3rd
  item: Lloyd RS

Site-directed deletion mutagenesis within the T4 endonuclease V gene: dispensable sequences within putative loop regions.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2067549
journal: Mutat Res
volume: 255
pages: 19-29
published year: 1991
authors:
  item: Dodson ML
  item: Prince MA
  item: Anderson WF
  item: Lloyd RS

Atomic structure of a pyrimidine-dimer specific excision-repair enzyme from bacteriophage T4.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1841278
journal: Nucleic Acids Symp Ser
volume: 4
pages: 181-4
published year: 1991
authors:
  item: Morikawa K
  item: Matsumoto O
  item: Tsujimoto M
  item: Katayanagi K
  item: Doi T
  item: Ariyoshi M
  item: Ikehara M
  item: Inaoka T
  item: Ohtsuka E

Participation of glutamic acid 23 of T4 endonuclease V in the beta-elimination reaction of an abasic site in a synthetic duplex DNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1357629
journal: Nucleic Acids Res
volume: 20
pages: 4761-4
published year: 1992
authors:
  item: Hori N
  item: Doi T
  item: Karaki Y
  item: Kikuchi M
  item: Ikehara M
  item: Ohtsuka E

Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/1409651
journal: Proc Natl Acad Sci U S A
volume: 89
pages: 9420-4
published year: 1992
authors:
  item: Doi T
  item: Recktenwald A
  item: Karaki Y
  item: Kikuchi M
  item: Morikawa K
  item: Ikehara M
  item: Inaoka T
  item: Hori N
  item: Ohtsuka E

X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/1575827
journal: Science
volume: 256
pages: 523-6
published year: 1992
authors:
  item: Morikawa K
  item: Matsumoto O
  item: Tsujimoto M
  item: Katayanagi K
  item: Ariyoshi M
  item: Doi T
  item: Ikehara M
  item: Inaoka T
  item: Ohtsuka E
references: P04418

Evidence for an imino intermediate in the T4 endonuclease V reaction.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8347626
journal: Biochemistry
volume: 32
pages: 8284-90
published year: 1993
authors:
  item: Dodson ML
  item: Schrock RD 3rd
  item: Lloyd RS

Structure/function analysis of the Ala116-->Lys121 region of endonuclease V by random targeted mutagenesis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8441681
journal: Nucleic Acids Res
volume: 21
pages: 727-32
published year: 1993
authors:
  item: Green AP
  item: deRiel JK
  item: Henderson EE

T4 endonuclease V. Perspectives on catalysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7916555
journal: Ann N Y Acad Sci
volume: 26
pages: 181-96
published year: 1994
authors:
  item: Latham KA
  item: Lloyd RS

Crystal structure of T4 endonuclease V. An excision repair enzyme for a pyrimidine dimer.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8092676
journal: Ann N Y Acad Sci
volume: 26
pages: 198-207
published year: 1994
authors:
  item: Morikawa K
  item: Ariyoshi M
  item: Vassylyev D
  item: Katayanagi K
  item: Nakamura H
  item: Doi T
  item: Hori N
  item: Ohtsuka E

Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8286363
journal: Biochemistry
volume: 33
pages: 57-64
published year: 1994
authors:
  item: Lee BJ
  item: Sakashita H
  item: Ohkubo T
  item: Ikehara M
  item: Doi T
  item: Morikawa K
  item: Kyogoku Y
  item: Osafune T
  item: Iwai S
  item: Ohtsuka E

Reaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7718562
journal: Biochemistry
volume: 34
pages: 4601-9
published year: 1995
authors:
  item: Iwai S
  item: Maeda M
  item: Shirai M
  item: Shimada Y
  item: Osafune T
  item: Murata T
  item: Ohtsuka E

Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/8521494
journal: Cell
volume: 83
pages: 773-82
published year: 1995
authors:
  item: Vassylyev DG
  item: Kashiwagi T
  item: Mikami Y
  item: Ariyoshi M
  item: Iwai S
  item: Ohtsuka E
  item: Morikawa K
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Involvement of glutamic acid 23 in the catalytic mechanism of T4 endonuclease V.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7852333
journal: J Biol Chem
volume: 270
pages: 2652-61
published year: 1995
authors:
  item: Manuel RC
  item: Latham KA
  item: Dodson ML
  item: Lloyd RS

Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/7783199
journal: J Mol Biol
volume: 249
pages: 360-75
published year: 1995
authors:
  item: Morikawa K
  item: Ariyoshi M
  item: Vassylyev DG
  item: Matsumoto O
  item: Katayanagi K
  item: Ohtsuka E
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Structural determinants for specific recognition by T4 endonuclease V.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8943268
journal: J Biol Chem
volume: 271
pages: 32147-52
published year: 1996
authors:
  item: McCullough AK
  item: Scharer O
  item: Verdine GL
  item: Lloyd RS

Role of specific amino acid residues in T4 endonuclease V that alter nontarget DNA binding.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9100001
journal: Biochemistry
volume: 36
pages: 4080-8
published year: 1997
authors:
  item: Nyaga SG
  item: Dodson ML
  item: Lloyd RS

The role of base flipping in damage recognition and catalysis by T4 endonuclease V.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9341165
journal: J Biol Chem
volume: 272
pages: 27210-7
published year: 1997
authors:
  item: McCullough AK
  item: Dodson ML
  item: Scharer OD
  item: Lloyd RS

Characterization of a novel cis-syn and trans-syn-II pyrimidine dimer glycosylase/AP lyase from a eukaryotic algal virus, Paramecium bursaria chlorella virus-1.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9582353
journal: J Biol Chem
volume: 273
pages: 13136-42
published year: 1998
authors:
  item: McCullough AK
  item: Romberg MT
  item: Nyaga S
  item: Wei Y
  item: Wood TG
  item: Taylor JS
  item: Van Etten JL
  item: Dodson ML
  item: Lloyd RS

Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10946233
journal: Mutat Res
volume: 460
pages: 257-75
published year: 2000
authors:
  item: Morikawa K
  item: Shirakawa M

Processivity of DNA repair enzymes.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11265291
journal: Methods Mol Biol
volume: 60
pages: 3-14
published year: 2001
authors:
  item: Lloyd RS

Interaction of T4 endonuclease V with DNA: importance of the flexible loop regions in protein-DNA interaction.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12783877
journal: J Biol Chem
volume: 278
pages: 30985-92
published year: 2003
authors:
  item: Ahn HC
  item: Ohkubo T
  item: Iwai S
  item: Morikawa K
  item: Lee BJ

ReferenceForCatalyticMechanism
reference index: 23
reference section: Fig.1, p.32152

ReferenceForCatalyticMechanism
reference index: 25
reference section: p.258-261