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Description:
DNA polymerase IV (EC 2.7.7.7) (Pol IV).
Molecular weight: 39516
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 )
Important dates:
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 1.
07-MAR-2006, entry version 52.
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 DPO4_ECOLI:
| Database | Pointer | Add. info#1 | Add. info#2 |
| EMBL | D38582 | BAA07593.1 | - |
| EMBL | U00096 | AAC73335.1 | - |
| EMBL | D83536 | BAA77901.1 | - |
| EMBL | U70214 | AAB08651.1 | - |
| EMBL | AF483080 | AAL91943.1 | - |
| EMBL | AF483081 | AAL91944.1 | - |
| EMBL | AF483082 | AAL91945.1 | - |
| EMBL | AF483083 | AAL91946.1 | - |
| EMBL | AF483084 | AAL91947.1 | - |
| EMBL | AF483085 | AAL91948.1 | - |
| EMBL | AF483086 | AAL91949.1 | - |
| EMBL | AF483087 | AAL91950.1 | - |
| EMBL | AF483088 | AAL91951.1 | - |
| EMBL | AF483089 | AAL91952.1 | - |
| EMBL | AF483090 | AAL91953.1 | - |
| EMBL | AF483091 | AAL91954.1 | - |
| EMBL | AF483092 | AAL91955.1 | - |
| EMBL | AF483093 | AAL91956.1 | - |
| EMBL | AF483094 | AAL91957.1 | - |
| EMBL | AF483095 | AAL91958.1 | - |
| EMBL | AF483096 | AAL91959.1 | - |
| EMBL | AF483097 | AAL91960.1 | - |
| EMBL | AF483098 | AAL91961.1 | - |
| EMBL | AF483099 | AAL91962.1 | - |
| EMBL | AF483100 | AAL91963.1 | - |
| EMBL | AF483101 | AAL91964.1 | - |
| EMBL | AF483102 | AAL91965.1 | - |
| EMBL | AF483103 | AAL91966.1 | - |
| EMBL | AF483104 | AAL91967.1 | - |
| EMBL | AF483105 | AAL91968.1 | - |
| PDB | 1OK7 | X-ray | C=336-351. |
| PDB | 1UNN | X-ray | C/D=243-351. |
| GenomeReviews | U00096_GR | b0231.1 | |
| EchoBASE | EB2935 | -.1 | |
| EcoGene | EG13141 | dinB. | |
| BioCyc | EcoCyc:G6115-MONOMER | -.1 | |
| HAMAP | MF_01113 | - | 1. |
| InterPro | IPR001126 | UMUC_like. | |
| Pfam | PF00817 | IMS | 1. |
| PROSITE | PS50173 | UMUC | 1. |
Keywords:
3D-structure; Complete proteome; DNA damage; DNA repair; DNA replication; DNA-binding; DNA-directed DNA polymerase; Magnesium; Metal-binding; Mutator protein; Nucleotidyltransferase; Transferase.
References:
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110;
RX MEDLINE=95319428; PubMed=7596361; DOI=10.1016/0165-7992(95)90024-1;
RA Ohmori H., Hatada E., Qiao Y., Tsuji M., Fukuda R.;
RT "dinP, a new gene in Escherichia coli, whose product shows
RT similarities to UmuC and its homologues.";
RL Mutat. Res. 347:1-7(1995).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the
RT 4.0 - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 7-342.
RC STRAIN=ECOR 10A, ECOR 13A, ECOR 17A, ECOR 1A, ECOR 20A, ECOR 23A,
RC ECOR 24A, ECOR 26B1, ECOR 27B1, ECOR 34B1, ECOR 35D, ECOR 37UG,
RC ECOR 45B1, ECOR 46D, ECOR 49D, ECOR 4A, ECOR 50D, ECOR 51B2,
RC ECOR 52B2, ECOR 57B2, ECOR 58B1, ECOR 59B2, ECOR 60B2, ECOR 62B2,
RC ECOR 68B1, and ECOR 70B1;
RA Bjedov I., Matic I., Denamur E.;
RT "Phylogeny of SOS inducible DNA polymerases of Escherichia coli.";
RL Submitted (FEB-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION.
RC STRAIN=K12;
RX MEDLINE=98054314; PubMed=9391106; DOI=10.1073/pnas.94.25.13792;
RA Kim S.-R., Maenhaut-Michel G., Yamada M., Yamamoto Y., Matsui K.,
RA Sofuni T., Nohmi T., Ohmori H.;
RT "Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an
RT overexpression of dinB/dinP results in strongly enhancing mutagenesis
RT in the absence of any exogenous treatment to damage DNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:13792-13797(1997).
RN [7]
RP FUNCTION.
RC STRAIN=K12 / MG1655;
RX MEDLINE=20532518; PubMed=11080171; DOI=10.1093/emboj/19.22.6259;
RA Napolitano R., Janel-Bintz R., Wagner J., Fuchs R.P.P.;
RT "All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V)
RT are involved in induced mutagenesis.";
RL EMBO J. 19:6259-6265(2000).
RN [8]
RP FUNCTION.
RX MEDLINE=21394634; PubMed=11463382; DOI=10.1016/S1097-2765(01)00204-0;
RA McKenzie G.J., Lee P.L., Lombardo M.-J., Hastings P.J.,
RA Rosenberg S.M.;
RT "SOS mutator DNA polymerase IV functions in adaptive mutation and not
RT adaptive amplification.";
RL Mol. Cell 7:571-579(2001).
RN [9]
RP FUNCTION.
RX MEDLINE=21657087; PubMed=11751576; DOI=10.1093/embo-reports/kvf007;
RA Lenne-Samuel N., Wagner J., Etienne H., Fuchs R.P.P.;
RT "The processivity factor beta controls DNA polymerase IV traffic
RT during spontaneous mutagenesis and translesion synthesis in vivo.";
RL EMBO Rep. 3:45-49(2002).
RN [10]
RP FUNCTION.
RC STRAIN=K12 / W3110;
RX MEDLINE=22080152; PubMed=12060704; DOI=10.1073/pnas.092269199;
RA Yeiser B., Pepper E.D., Goodman M.F., Finkel S.E.;
RT "SOS-induced DNA polymerases enhance long-term survival and
RT evolutionary fitness.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:8737-8741(2002).
RN [11]
RP CHARACTERIZATION.
RX MEDLINE=80234712; PubMed=6771759;
RA Kenyon C.J., Walker G.C.;
RT "DNA-damaging agents stimulate gene expression at specific loci in
RT Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 77:2819-2823(1980).
RN [12]
RP CHARACTERIZATION, AND MUTAGENESIS OF ASP-8; ARG-49; ASP-103 AND
RP GLU-104.
RC STRAIN=K12;
RX MEDLINE=99417968; PubMed=10488344; DOI=10.1016/S1097-2765(00)80376-7;
RA Wagner J., Gruz P., Kim S.-R., Yamada M., Matsui K., Fuchs R.P.P.,
RA Nohmi T.;
RT "The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV,
RT involved in mutagenesis.";
RL Mol. Cell 4:281-286(1999).
RN [13]
RP REVIEW.
RX MEDLINE=21479116; PubMed=11595180; DOI=10.1016/S0092-8674(01)00509-8;
RA Friedberg E.C., Fischhaber P.L., Kisker C.;
RT "Error-prone DNA polymerases: novel structures and the benefits of
RT infidelity.";
RL Cell 107:9-12(2001).
RN [14]
RP REVIEW.
RX MEDLINE=21472196; PubMed=11587937; DOI=10.1016/S1369-5274(00)00255-1;
RA McKenzie G.J., Rosenberg S.M.;
RT "Adaptive mutations, mutator DNA polymerases and genetic change
RT strategies of pathogens.";
RL Curr. Opin. Microbiol. 4:586-594(2001).
RN [15]
RP REVIEW.
RX MEDLINE=22039708; PubMed=12045089;
RX DOI=10.1146/annurev.biochem.71.083101.124707;
RA Goodman M.F.;
RT "Error-prone repair DNA polymerases in prokaryotes and eukaryotes.";
RL Annu. Rev. Biochem. 71:17-50(2002).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 243-351 IN COMPLEX WITH DNAN.
RX PubMed=14592985; DOI=10.1093/emboj/cdg568;
RA Bunting K.A., Roe S.M., Pearl L.H.;
RT "Structural basis for recruitment of translesion DNA polymerase Pol
RT IV/DinB to the beta-clamp.";
RL EMBO J. 22:5883-5892(2003).
Feature:
CHAIN 1 351 DNA polymerase IV.
/FTId=PRO_0000173912.
DOMAIN 4 185 UmuC.
ACT_SITE 104 104 By similarity.
METAL 8 8 Magnesium (By similarity).
METAL 103 103 Magnesium (By similarity).
SITE 13 13 Substrate discrimination (By similarity).
VARIANT 36 38 ERR -> ARG (in strain: ECOR 45B1).
VARIANT 124 124 Q -> K (in strain: ECOR 35D).
VARIANT 132 132 N -> S (in strain: ECOR 34B1 and ECOR
37UG).
VARIANT 135 135 Q -> H (in strain: ECOR 70B1).
VARIANT 170 170 P -> S (in strain: ECOR 37UG).
VARIANT 171 171 A -> T (in strain: ECOR 45B1, ECOR 46D,
ECOR 49D and ECOR 50D).
VARIANT 176 176 L -> F (in strain: ECOR 37UG).
VARIANT 201 201 G -> S (in strain: ECOR 59B2).
VARIANT 210 210 M -> I (in strain: ECOR 37UG, ECOR 45B1,
ECOR 51B2, ECOR 52B2, ECOR 58B1 and ECOR
70B1).
VARIANT 210 210 M -> T (in strain: ECOR 35D, ECOR 46D,
ECOR 49D, ECOR 50D, ECOR 57B2, ECOR 59B2,
ECOR 60B2 and ECOR 62B2).
VARIANT 225 225 R -> C (in strain: ECOR 59B2 and ECOR
60B2).
VARIANT 310 310 A -> S (in strain: ECOR 57B2, ECOR 59B2,
ECOR 60B2 and ECOR 62B2).
VARIANT 321 321 D -> N (in strain: ECOR 35D).
MUTAGEN 8 8 D->A,H: Loss of function.
MUTAGEN 49 49 R->A,F: Loss of function.
MUTAGEN 103 103 D->A,N: Loss of function.
MUTAGEN 104 104 E->A: Loss of function.
STRAND 242 253
HELIX 256 277
TURN 279 280
STRAND 282 282
STRAND 284 292
TURN 293 294
STRAND 295 295
STRAND 297 303
STRAND 305 306
HELIX 309 323
TURN 325 326
STRAND 329 337
STRAND 346 346
Comments:
-!- FUNCTION: Poorly processive, error-prone DNA polymerase involved
in untargeted mutagenesis. Copies undamaged DNA at stalled
replication forks, which arise in vivo from mismatched or
misaligned primer ends. These misaligned primers can be extended
by polIV. Exhibits no 3'-5' exonuclease (proofreading) activity.
Overexpression of polIV results in increased frameshift
mutagenesis. It is required for stationary-phase adaptive
mutation, which provides the bacterium with flexibility in dealing
with environmental stress, enhancing long-term survival and
evolutionary fitness. May be involved in translesional synthesis,
in conjunction with the beta clamp from polIII.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1).
-!- COFACTOR: Binds 2 magnesium ions per subunit (By similarity).
-!- SUBUNIT: Monomer (Potential).
-!- SUBCELLULAR LOCATION: Cytoplasm (Probable).
-!- INDUCTION: By SOS response.
-!- DOMAIN: The catalytic core consists of fingers, palm and thumb
subdomains, but the fingers and thumb subdomains are much smaller
than in high-fidelity polymerases; residues from five sequence
motifs of the Y-family cluster around an active site cleft that
can accommodate DNA and nucleotide substrates with relaxed
geometric constraints, with consequently higher rates of
misincorporation and low processivity. It lacks the O helices
present in high-fidelity DNA polymerases in the fingers domain (By
similarity).
-!- SIMILARITY: Belongs to the DNA polymerase type-Y family.
-!- SIMILARITY: Contains 1 umuC domain.
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Sequence length: 351
MRKIIHVDMD CFFAAVEMRD NPALRDIPIA IGGSRERRGV ISTANYPARK FGVRSAMPTG
MALKLCPHLT LLPGRFDAYK EASNHIREIF SRYTSRIEPL SLDEAYLDVT DSVHCHGSAT
LIAQEIRQTI FNELQLTASA GVAPVKFLAK IASDMNKPNG QFVITPAEVP AFLQTLPLAK
IPGVGKVSAA KLEAMGLRTC GDVQKCDLVM LLKRFGKFGR ILWERSQGID ERDVNSERLR
KSVGVERTMA EDIHHWSECE AIIERLYPEL ERRLAKVKPD LLIARQGVKL KFDDFQQTTQ
EHVWPRLNKA DLIATARKTW DERRGGRGVR LVGLHVTLLD PQMERQLVLG L