EzCatDB: S00016

DB codeS00016
CATH domainDomain 11.10.440.10Catalytic domain
E.C.3.1.25.1
CSA1vas
MACiEM0162


Enzyme Name
Swiss-protKEGG

P04418
Protein nameEndonuclease Vdeoxyribonuclease (pyrimidine dimer)
endodeoxyribonuclease (pyrimidine dimer)
endodeoxyribonuclease (pyrimidine dimer)
bacteriophage T4 endodeoxyribonuclease V
T4 endonuclease V
SynonymsEC 3.1.25.1


Swiss-prot:Accession NumberP04418
Entry nameEND5_BPT4
ActivityEndonucleolytic cleavage near pyrimidine dimers to products with 5''-phosphate.
SubunitMonomer.
Subcellular location
Cofactor


SubstratesProducts
KEGG-idL00011C00001C00578L00013
Compoundcys-syn pyrimidine dimer in DNAH2ODNA 5'-phosphateDNA 3'-trans-alpha,beta unsaturated aldehyde
Typenucleic acidsH2Onucleic acids,phosphate group/phosphate ionnucleic acids,carbohydrate
1endAUnbound
UnboundUnbound
1eniAUnbound
UnboundUnbound
1enjAUnbound
UnboundUnbound
1enkAUnbound
UnboundUnbound
1vasABound:A-T-C-G-C-G-T-T-G-C-G-C-T(chain B)
UnboundUnbound
2endAUnbound
UnboundUnbound

Active-site residues
resource
Swiss-prot;P04418 & literature [20]
pdbCatalytic residuesMain-chain involved in catalysiscomment
1endAGLU  23;ARG 26
THR 2

1eniAGLU  23;ARG 26
THR 2

1enjA       ;ARG 26
THR 2
mutant E23Q
1enkA       ;ARG 26
THR 2
mutant E23D
1vasA       ;ARG 26
THR 2
mutant E23Q
2endAGLU  23;ARG 26
THR 2


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig. 1, p.51-54
[6]Scheme 1, p.17637-17638
[9]Fig.1
[10]Fig.1, p.9424
[11]p.524-525
[12]Fig.1
[14]Fig.8, p.182-193
[15]Fig.1, p.201-205
[17]Fig.1
[18]Fig.4, p.778-779
[19]Fig.1, p.2660-2661
[20]p.369-371
[21]

[23]Fig.1, p.32152
[25]p.258-261

references
[1]
PubMed ID3172233
JournalJ Mol Biol
Year1988
Volume202
Pages683-4
AuthorsMorikawa K, Tsujimoto M, Ikehara M, Inaoka T, Ohtsuka E
TitlePreliminary crystallographic study of pyrimidine dimer-specific excision-repair enzyme from bacteriophage T4.
[2]
PubMed ID2671706
JournalMutat Res
Year1989
Volume218
Pages49-65
AuthorsDodson ML, Lloyd RS
TitleStructure-function studies of the T4 endonuclease V repair enzyme.
[3]
PubMed ID2695926
JournalProteins
Year1989
Volume6
Pages128-38
AuthorsLloyd RS, Augustine ML
TitleSite-directed mutagenesis of the T4 endonuclease V gene: mutations which enhance enzyme specific activity at low salt concentrations.
[4]
PubMed ID1888726
JournalBiochemistry
Year1991
Volume30
Pages8638-48
AuthorsNickell C, Lloyd RS
TitleMutations in endonuclease V that affect both protein-protein association and target site location.
[5]
PubMed ID2037608
JournalJ Biol Chem
Year1991
Volume266
Pages10686-93
AuthorsPrince MA, Friedman B, Gruskin EA, Schrock RD 3rd, Lloyd RS
TitleSelective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding.
[6]
PubMed ID1894643
JournalJ Biol Chem
Year1991
Volume266
Pages17631-9
AuthorsSchrock RD 3rd, Lloyd RS
TitleReductive 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.
[7]
PubMed ID2067549
JournalMutat Res
Year1991
Volume255
Pages19-29
AuthorsDodson ML, Prince MA, Anderson WF, Lloyd RS
TitleSite-directed deletion mutagenesis within the T4 endonuclease V gene: dispensable sequences within putative loop regions.
[8]
PubMed ID1841278
JournalNucleic Acids Symp Ser
Year1991
Volume4
Pages181-4
AuthorsMorikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Doi T, Ariyoshi M, Ikehara M, Inaoka T, Ohtsuka E
TitleAtomic structure of a pyrimidine-dimer specific excision-repair enzyme from bacteriophage T4.
[9]
PubMed ID1357629
JournalNucleic Acids Res
Year1992
Volume20
Pages4761-4
AuthorsHori N, Doi T, Karaki Y, Kikuchi M, Ikehara M, Ohtsuka E
TitleParticipation of glutamic acid 23 of T4 endonuclease V in the beta-elimination reaction of an abasic site in a synthetic duplex DNA.
[10]
PubMed ID1409651
JournalProc Natl Acad Sci U S A
Year1992
Volume89
Pages9420-4
AuthorsDoi T, Recktenwald A, Karaki Y, Kikuchi M, Morikawa K, Ikehara M, Inaoka T, Hori N, Ohtsuka E
TitleRole of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
PubMed ID1575827
JournalScience
Year1992
Volume256
Pages523-6
AuthorsMorikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Ariyoshi M, Doi T, Ikehara M, Inaoka T, Ohtsuka E
TitleX-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer.
Related Swiss-protP04418
[12]
PubMed ID8347626
JournalBiochemistry
Year1993
Volume32
Pages8284-90
AuthorsDodson ML, Schrock RD 3rd, Lloyd RS
TitleEvidence for an imino intermediate in the T4 endonuclease V reaction.
[13]
PubMed ID8441681
JournalNucleic Acids Res
Year1993
Volume21
Pages727-32
AuthorsGreen AP, deRiel JK, Henderson EE
TitleStructure/function analysis of the Ala116-->Lys121 region of endonuclease V by random targeted mutagenesis.
[14]
PubMed ID7916555
JournalAnn N Y Acad Sci
Year1994
Volume26
Pages181-96
AuthorsLatham KA, Lloyd RS
TitleT4 endonuclease V. Perspectives on catalysis.
[15]
PubMed ID8092676
JournalAnn N Y Acad Sci
Year1994
Volume26
Pages198-207
AuthorsMorikawa K, Ariyoshi M, Vassylyev D, Katayanagi K, Nakamura H, Doi T, Hori N, Ohtsuka E
TitleCrystal structure of T4 endonuclease V. An excision repair enzyme for a pyrimidine dimer.
[16]
PubMed ID8286363
JournalBiochemistry
Year1994
Volume33
Pages57-64
AuthorsLee BJ, Sakashita H, Ohkubo T, Ikehara M, Doi T, Morikawa K, Kyogoku Y, Osafune T, Iwai S, Ohtsuka E
TitleNuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA.
[17]
PubMed ID7718562
JournalBiochemistry
Year1995
Volume34
Pages4601-9
AuthorsIwai S, Maeda M, Shirai M, Shimada Y, Osafune T, Murata T, Ohtsuka E
TitleReaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes.
[18]
CommentsX-ray crystallography
PubMed ID8521494
JournalCell
Year1995
Volume83
Pages773-82
AuthorsVassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K
TitleAtomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
Related PDB1vas
[19]
PubMed ID7852333
JournalJ Biol Chem
Year1995
Volume270
Pages2652-61
AuthorsManuel RC, Latham KA, Dodson ML, Lloyd RS
TitleInvolvement of glutamic acid 23 in the catalytic mechanism of T4 endonuclease V.
[20]
CommentsX-ray crystallography
PubMed ID7783199
JournalJ Mol Biol
Year1995
Volume249
Pages360-75
AuthorsMorikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E
TitleCrystal 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.
Related PDB1end,1eni,1enj,1enk,2end
[21]
PubMed ID8943268
JournalJ Biol Chem
Year1996
Volume271
Pages32147-52
AuthorsMcCullough AK, Scharer O, Verdine GL, Lloyd RS
TitleStructural determinants for specific recognition by T4 endonuclease V.
[22]
PubMed ID9100001
JournalBiochemistry
Year1997
Volume36
Pages4080-8
AuthorsNyaga SG, Dodson ML, Lloyd RS
TitleRole of specific amino acid residues in T4 endonuclease V that alter nontarget DNA binding.
[23]
PubMed ID9341165
JournalJ Biol Chem
Year1997
Volume272
Pages27210-7
AuthorsMcCullough AK, Dodson ML, Scharer OD, Lloyd RS
TitleThe role of base flipping in damage recognition and catalysis by T4 endonuclease V.
[24]
PubMed ID9582353
JournalJ Biol Chem
Year1998
Volume273
Pages13136-42
AuthorsMcCullough AK, Romberg MT, Nyaga S, Wei Y, Wood TG, Taylor JS, Van Etten JL, Dodson ML, Lloyd RS
TitleCharacterization of a novel cis-syn and trans-syn-II pyrimidine dimer glycosylase/AP lyase from a eukaryotic algal virus, Paramecium bursaria chlorella virus-1.
[25]
PubMed ID10946233
JournalMutat Res
Year2000
Volume460
Pages257-75
AuthorsMorikawa K, Shirakawa M
TitleThree-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein, and human nucleotide excision repair factor XPA.
[26]
PubMed ID11265291
JournalMethods Mol Biol
Year2001
Volume60
Pages3-14
AuthorsLloyd RS
TitleProcessivity of DNA repair enzymes.
[27]
PubMed ID12783877
JournalJ Biol Chem
Year2003
Volume278
Pages30985-92
AuthorsAhn HC, Ohkubo T, Iwai S, Morikawa K, Lee BJ
TitleInteraction of T4 endonuclease V with DNA: importance of the flexible loop regions in protein-DNA interaction.

comments
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).

createdupdated
2004-03-192009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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