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Description:
Endonuclease VIII (DNA glycosylase/AP lyase Nei) (EC 3.2.2.-)(EC 4.2.99.18) (DNA-(apurinic or apyrimidinic site) lyase Nei).
Molecular weight: 29714
View which proteins in this organism that is involved with DNA Repair;
classified after biological processes (using data from the GOA project):
DNA repair( GO:0006281 ) base-excision repair( GO:0006284 )
Important dates:
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
15-JUL-1998, sequence version 2.
07-MAR-2006, entry version 55.
Phylogenetic order:
Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia.
To calculate the pI (Isoelectric point - the pH where a protein has a neutral charge),
go to this page and enter the protein ID (e.g 3MG_ECOLI): http://us.expasy.org/tools/pi_tool.html
Links to references in other databases for protein END8_ECOLI:
| Database | Pointer | Add. info#1 | Add. info#2 |
| EMBL | U38616 | AAC45355.1 | - |
| EMBL | D89754 | BAA20414.1 | - |
| EMBL | D90710 | BAA35378.1 | - |
| EMBL | U00096 | AAC73808.1 | - |
| PIR | A64807 | A64807. | |
| PDB | 1K3W | X-ray | A=1-262. |
| PDB | 1K3X | X-ray | A=1-262. |
| PDB | 1Q39 | X-ray | A=1-262. |
| PDB | 1Q3B | X-ray | A=1-262. |
| PDB | 1Q3C | X-ray | A=1-262. |
| GenomeReviews | U00096_GR | b0714.1 | |
| EchoBASE | EB3026 | -.1 | |
| EcoGene | EG13237 | nei. | |
| BioCyc | EcoCyc:G6383-MONOMER | -.1 | |
| GO | GO:0005515 | F:protein binding | IPI. |
| HAMAP | MF_01253 | - | 1. |
| InterPro | IPR000191 | Fapy_DNA_glyco. | |
| InterPro | IPR012319 | Form_DNAglyc_cat. | |
| InterPro | IPR000214 | Fpg_Zn_BS. | |
| InterPro | IPR010663 | Znf_Fpg. | |
| Pfam | PF01149 | Fapy_DNA_glyco | 1. |
| Pfam | PF06831 | H2TH | 1. |
| Pfam | PF06827 | zf-FPG_IleRS | 1. |
| ProDom | PD003680 | Fapy_DNA_glyco | 1. |
| PROSITE | PS51068 | FPG_CAT | 1. |
| PROSITE | PS01242 | ZF_FPG_1 | 1. |
| PROSITE | PS51066 | ZF_FPG_2 | 1. |
Keywords:
3D-structure; Complete proteome; Direct protein sequencing; DNA damage; DNA repair; DNA-binding; Glycosidase; Hydrolase; Lyase; Metal-binding; Multifunctional enzyme; Zinc; Zinc-finger.
References:
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-35;
RP 188-205 AND 213-226.
RX MEDLINE=97315255; PubMed=9171429;
RA Jiang D., Hatahet Z., Blaisdell J.O., Melamede R.J., Wallace S.S.;
RT "Escherichia coli endonuclease VIII: cloning, sequencing, and
RT overexpression of the nei structural gene and characterization of nei
RT and nei nth mutants.";
RL J. Bacteriol. 179:3773-3782(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX MEDLINE=97315256; PubMed=9171430;
RA Saito Y., Uraki F., Nakajima S., Asaeda A., Ono K., Kubo K.,
RA Yamamoto K.;
RT "Characterization of endonuclease III (nth) and endonuclease VIII
RT (nei) mutants of Escherichia coli K-12.";
RL J. Bacteriol. 179:3783-3785(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110;
RX MEDLINE=97061202; PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
RA Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
RA Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
RA Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
RA Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
RA Yano M., Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome
RT corresponding to the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655;
RX MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA Mau B., Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1474(1997).
RN [5]
RP MUTAGENESIS OF PRO-1; GLU-2; GLU-5; ASP-128; ASP-159 AND GLU-173.
RX PubMed=11711552; DOI=10.1074/jbc.M110499200;
RA Burgess S., Jaruga P., Dodson M.L., Dizdaroglu M., Lloyd R.S.;
RT "Determination of active site residues in Escherichia coli
RT endonuclease VIII.";
RL J. Biol. Chem. 277:2938-2944(2002).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.42 ANGSTROMS) IN COMPLEX WITH DNA, AND
RP MUTAGENESIS OF GLU-2; LYS-52; ARG-212 AND ARG-252.
RX PubMed=11847126; DOI=10.1093/emboj/21.4.789;
RA Zharkov D.O., Golan G., Gilboa R., Fernandes A.S., Gerchman S.E.,
RA Kycia J.H., Rieger R.A., Grollman A.P., Shoham G.;
RT "Structural analysis of an Escherichia coli endonuclease VIII covalent
RT reaction intermediate.";
RL EMBO J. 21:789-800(2002).
Feature:
INIT_MET 0 0
CHAIN 1 262 Endonuclease VIII.
/FTId=PRO_0000170893.
ZN_FING 228 262 FPG-type.
ACT_SITE 1 1 Schiff-base intermediate with DNA.
ACT_SITE 2 2 Proton donor (Probable).
ACT_SITE 52 52 Proton donor (in beta-elimination)
(Probable).
ACT_SITE 252 252 Proton donor (in delta-elimination)
(Probable).
BINDING 69 69 DNA.
BINDING 124 124 DNA.
BINDING 168 168 DNA.
MUTAGEN 1 1 P->T: Loss of glycosylase and AP lyase
activity.
MUTAGEN 2 2 E->A,Q: Loss of glycosylase activity. No
effect on AP lyase activity.
MUTAGEN 2 2 E->D: Much reduced glycosylase activity.
No effect on AP lyase activity.
MUTAGEN 5 5 E->Q: Reduced glycosylase activity. No
effect on AP lyase activity.
MUTAGEN 52 52 K->A: Loss of DNA cleavage at sites
containing oxidized pyrimidine. No effect
on AP lyase activity.
MUTAGEN 128 128 D->N: Reduced glycosylase activity. No
effect on AP lyase activity.
MUTAGEN 159 159 D->N: No effect on glycosylase and AP
lyase activity.
MUTAGEN 173 173 E->Q: Loss of glycosylase activity. No
effect on AP lyase activity.
MUTAGEN 212 212 R->A: Slightly reduced activity.
MUTAGEN 252 252 R->A: Reduced DNA cleavage at sites
containing oxidized pyrimidine. No effect
on AP lyase activity.
HELIX 3 17
STRAND 18 18
TURN 19 19
STRAND 23 29
HELIX 30 39
TURN 40 41
STRAND 44 50
TURN 51 52
STRAND 53 58
TURN 59 60
STRAND 61 61
STRAND 63 67
TURN 69 71
STRAND 73 78
TURN 79 80
STRAND 86 87
STRAND 89 94
STRAND 96 104
STRAND 107 111
TURN 113 114
HELIX 115 118
STRAND 119 119
HELIX 120 124
STRAND 128 128
TURN 129 130
TURN 132 133
HELIX 136 144
STRAND 145 145
TURN 146 150
STRAND 151 151
HELIX 153 156
TURN 157 158
TURN 160 162
STRAND 163 164
TURN 165 165
HELIX 168 178
TURN 179 179
STRAND 182 183
HELIX 186 188
STRAND 189 189
HELIX 191 211
STRAND 228 229
TURN 230 231
TURN 233 234
STRAND 235 236
TURN 238 240
STRAND 243 243
STRAND 245 249
TURN 250 251
STRAND 252 256
TURN 258 260
Comments:
-!- FUNCTION: Involved in base excision repair of DNA damaged by
oxidation or by mutagenic agents. Acts as DNA glycosylase that
recognizes and removes damaged bases. Has a preference for
oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracyl
and 5,6-dihydrothymine. Has AP (apurinic/apyrimidinic) lyase
activity and introduces nicks in the DNA strand. Cleaves the DNA
backbone by beta-delta elimination to generate a single-strand
break at the site of the removed base with both 3'- and 5'-
phosphates.
-!- CATALYTIC ACTIVITY: Removes damaged bases from DNA, leaving an
abasic site.
-!- CATALYTIC ACTIVITY: The C-O-P bond 3' to the apurinic or
apyrimidinic site in DNA is broken by a beta-elimination reaction,
leaving a 3'-terminal unsaturated sugar and a product with a
terminal 5'-phosphate.
-!- COFACTOR: Binds 1 zinc ion per subunit.
-!- INTERACTION:
P0A6F5:groL; NbExp=1; IntAct=EBI-555110, EBI-543750;
P02341:hupB; NbExp=1; IntAct=EBI-555110, EBI-370411;
P00391:lpdA; NbExp=1; IntAct=EBI-555110, EBI-542856;
P68739:nfi; NbExp=1; IntAct=EBI-555110, EBI-551698;
P60723:rplD; NbExp=1; IntAct=EBI-555110, EBI-545597;
P02422:rplU; NbExp=1; IntAct=EBI-555110, EBI-542445;
P0A7M2:rpmB; NbExp=1; IntAct=EBI-555110, EBI-543024;
P0A7V8:rpsD; NbExp=1; IntAct=EBI-555110, EBI-543939;
P02370:rpsN; NbExp=1; IntAct=EBI-555110, EBI-543971;
P30856:slyD; NbExp=1; IntAct=EBI-555110, EBI-369251;
-!- SIMILARITY: Belongs to the FPG family.
-!- SIMILARITY: Contains 1 FPG-type zinc finger.
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Sequence length: 262
PEGPEIRRAA DNLEAAIKGK PLTDVWFAFP QLKPYQSQLI GQHVTHVETR GKALLTHFSN
DLTLYSHNQL YGVWRVVDTG EEPQTTRVLR VKLQTADKTI LLYSASDIEM LTPEQLTTHP
FLQRVGPDVL DPNLTPEVVK ERLLSPRFRN RQFAGLLLDQ AFLAGLGNYL RVEILWQVGL
TGNHKAKDLN AAQLDALAHA LLEIPRFSYA TRGQVDENKH HGALFRFKVF HRDGEPCERC
GSIIEKTTLS SRPFYWCPGC QH