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Q97W02 (DPO4_SULSO) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA polymerase IV

Short name=Pol IV
EC=2.7.7.7
Gene names
Name:dbh
Synonyms:dpo4
Ordered Locus Names:SSO2448
OrganismSulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) [Reference proteome] [HAMAP]
Taxonomic identifier273057 [NCBI]
Taxonomic lineageArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus

Protein attributes

Sequence length352 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (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. It is involved in translesional synthesis. HAMAP-Rule MF_01113

Catalytic activity

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). HAMAP-Rule MF_01113

Cofactor

Binds 2 magnesium ions per subunit.

Subunit structure

Monomer. Interacts with the PCNA heterotrimer via PCNA1. Ref.5

Subcellular location

Cytoplasm Probable HAMAP-Rule MF_01113.

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. HAMAP-Rule MF_01113

Sequence similarities

Belongs to the DNA polymerase type-Y family.

Contains 1 umuC domain.

Biophysicochemical properties

Temperature dependence:

Highly active from 35 to 95 degrees Celsius. Thermostable. HAMAP-Rule MF_01113

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 352352DNA polymerase IV HAMAP-Rule MF_01113
PRO_0000173976

Regions

Domain3 – 187185UmuC

Sites

Active site1061
Metal binding71Magnesium
Metal binding1051Magnesium
Site121Substrate discrimination

Experimental info

Mutagenesis105 – 1062DE → AA: Loss of function. Ref.4
Mutagenesis342 – 35211Missing: Almost complete loss of interaction with PCNA. Ref.4 Ref.5

Secondary structure

.................................................................... 352
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q97W02 [UniParc].

Last modified October 1, 2001. Version 1.
Checksum: C0B0AD4B3A3E87D0

FASTA35240,193
        10         20         30         40         50         60 
MIVLFVDFDY FYAQVEEVLN PSLKGKPVVV CVFSGRFEDS GAVATANYEA RKFGVKAGIP 

        70         80         90        100        110        120 
IVEAKKILPN AVYLPMRKEV YQQVSSRIMN LLREYSEKIE IASIDEAYLD ISDKVRDYRE 

       130        140        150        160        170        180 
AYNLGLEIKN KILEKEKITV TVGISKNKVF AKIAADMAKP NGIKVIDDEE VKRLIRELDI 

       190        200        210        220        230        240 
ADVPGIGNIT AEKLKKLGIN KLVDTLSIEF DKLKGMIGEA KAKYLISLAR DEYNEPIRTR 

       250        260        270        280        290        300 
VRKSIGRIVT MKRNSRNLEE IKPYLFRAIE ESYYKLDKRI PKAIHVVAVT EDLDIVSRGR 

       310        320        330        340        350 
TFPHGISKET AYSESVKLLQ KILEEDERKI RRIGVRFSKF IEAIGLDKFF DT 

« Hide

References

« Hide 'large scale' references
[1]"The complete genome of the crenarchaeon Sulfolobus solfataricus P2."
She Q., Singh R.K., Confalonieri F., Zivanovic Y., Allard G., Awayez M.J., Chan-Weiher C.C.-Y., Clausen I.G., Curtis B.A., De Moors A., Erauso G., Fletcher C., Gordon P.M.K., Heikamp-de Jong I., Jeffries A.C., Kozera C.J., Medina N., Peng X. expand/collapse author list , Thi-Ngoc H.P., Redder P., Schenk M.E., Theriault C., Tolstrup N., Charlebois R.L., Doolittle W.F., Duguet M., Gaasterland T., Garrett R.A., Ragan M.A., Sensen C.W., Van der Oost J.
Proc. Natl. Acad. Sci. U.S.A. 98:7835-7840(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[2]"Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic pol eta."
Boudsocq F., Iwai S., Hanaoka F., Woodgate R.
Nucleic Acids Res. 29:4607-4616(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[3]"Low fidelity DNA synthesis by a Y family DNA polymerase due to misalignment in the active site."
Kokoska R.J., Bebenek K., Boudsocq F., Woodgate R., Kunkel T.A.
J. Biol. Chem. 277:19633-19638(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[4]"Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication."
Ling H., Boudsocq F., Woodgate R., Yang W.
Cell 107:91-102(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF TERNARY COMPLEX WITH DNA AND AN INCOMING NUCLEOTIDE, MUTAGENESIS OF 105-ASP-GLU-106.
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
[5]"Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA."
Xing G., Kirouac K., Shin Y.J., Bell S.D., Ling H.
Mol. Microbiol. 71:678-691(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 1-244 IN COMPLEX WITH PCNA, INTERACTION WITH PCNA1, SUBUNIT, DNA-BINDING, MUTAGENESIS OF 342-GLU--THR-352.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE006641 Genomic DNA. Translation: AAK42588.1.
PIRE90416.
RefSeqNP_343798.1. NC_002754.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JX4X-ray1.70A1-352[»]
1JXLX-ray2.10A1-352[»]
1N48X-ray2.20A1-352[»]
1N56X-ray2.40A/B1-352[»]
1RYRX-ray2.28A1-352[»]
1RYSX-ray2.03A/B1-352[»]
1S0MX-ray2.70A/B1-352[»]
1S0NX-ray2.80A1-352[»]
1S0OX-ray2.10A/B1-352[»]
1S10X-ray2.10A1-352[»]
1S97X-ray2.40A/B/C/D1-352[»]
1S9FX-ray2.00A/B/C/D1-352[»]
2AGOX-ray2.85A1-341[»]
2AGPX-ray2.90A/B1-341[»]
2AGQX-ray2.10A1-341[»]
2ASDX-ray1.95A/B2-352[»]
2ASJX-ray2.35A/B2-352[»]
2ASLX-ray2.65A/B2-352[»]
2ATLX-ray2.80A/B2-352[»]
2AU0X-ray2.70A/B2-352[»]
2BQ3X-ray2.00A1-352[»]
2BQRX-ray2.37A1-352[»]
2BQUX-ray2.50A1-352[»]
2BR0X-ray2.17A1-352[»]
2C22X-ray2.56A1-352[»]
2C28X-ray2.27A1-352[»]
2C2DX-ray2.57A1-352[»]
2C2EX-ray2.61A1-352[»]
2C2RX-ray2.55A1-352[»]
2IA6X-ray2.50A/B1-352[»]
2IBKX-ray2.25A1-352[»]
2IMWX-ray2.05P1-348[»]
2J6SX-ray2.50A1-352[»]
2J6TX-ray2.60A1-352[»]
2J6UX-ray2.50A1-352[»]
2JEFX-ray2.17A1-352[»]
2JEGX-ray2.38A1-352[»]
2JEIX-ray2.39A1-352[»]
2JEJX-ray1.86A1-352[»]
2R8GX-ray2.70A1-352[»]
2R8HX-ray2.48A1-352[»]
2R8IX-ray2.38A1-352[»]
2RDIX-ray1.92A1-341[»]
2RDJX-ray2.20A/B1-352[»]
2UVRX-ray2.90A1-352[»]
2UVUX-ray2.70A1-352[»]
2UVVX-ray2.20A1-352[»]
2UVWX-ray2.09A1-352[»]
2V4QX-ray2.60A1-352[»]
2V4RX-ray2.50A1-352[»]
2V9WX-ray3.00A/B1-352[»]
2VA2X-ray2.80A/B1-352[»]
2VA3X-ray2.98A1-352[»]
2W8KX-ray3.10A1-352[»]
2W8LX-ray3.00A1-352[»]
2W9AX-ray2.60A1-352[»]
2W9BX-ray2.28A/B1-352[»]
2W9CX-ray2.87A/B1-352[»]
2XC9X-ray2.20A1-352[»]
2XCAX-ray2.50A1-352[»]
2XCPX-ray2.60A/B1-352[»]
3FDSX-ray2.05A1-352[»]
3GIIX-ray2.60A2-341[»]
3GIJX-ray2.40A/B2-341[»]
3GIKX-ray2.90A2-341[»]
3GILX-ray2.71A/B2-341[»]
3GIMX-ray2.70A2-341[»]
3KHGX-ray2.96A/B2-341[»]
3KHHX-ray2.70A/B2-341[»]
3KHLX-ray2.10A/B2-341[»]
3KHRX-ray2.01A/B2-341[»]
3M9MX-ray2.90B1-352[»]
3M9NX-ray1.93B1-352[»]
3M9OX-ray2.00B1-352[»]
3PR4X-ray2.65A1-341[»]
3PR5X-ray2.40B1-341[»]
3PVXX-ray3.03A1-341[»]
3PW0X-ray2.91A1-341[»]
3PW2X-ray2.74A1-341[»]
3PW4X-ray2.90A1-341[»]
3PW5X-ray3.00A1-341[»]
3PW7X-ray2.90A/E1-341[»]
3QZ7X-ray2.00A1-352[»]
3QZ8X-ray2.00A1-352[»]
3RAQX-ray2.25A/B2-341[»]
3RAXX-ray1.89A/B2-341[»]
3RB0X-ray3.22A/B2-341[»]
3RB3X-ray2.80A2-341[»]
3RB4X-ray2.80A/B2-341[»]
3RB6X-ray2.70A/B2-341[»]
3RBDX-ray2.50A/B2-341[»]
3RBEX-ray2.80A/B2-341[»]
3T5HX-ray2.35A1-341[»]
3T5JX-ray2.40A1-341[»]
3T5KX-ray2.90A1-341[»]
3T5LX-ray2.90A1-341[»]
3V6HX-ray2.30A/B1-342[»]
3V6JX-ray2.30A/J1-342[»]
3V6KX-ray3.60A/J1-342[»]
4F4WX-ray1.90A/B231-352[»]
4F4XX-ray2.05A231-352[»]
4F4YX-ray2.34A/B5-211[»]
A/B127-335[»]
4F4ZX-ray2.30A/B1-246[»]
4F50X-ray2.22A246-352[»]
4FBTX-ray2.00A1-341[»]
4FBUX-ray2.60A/B1-341[»]
4G3IX-ray2.50A/B1-341[»]
4GC6X-ray2.90A1-352[»]
4GC7X-ray2.89A/B1-352[»]
4JUZX-ray2.65A1-341[»]
4JV0X-ray2.95A1-341[»]
4JV1X-ray2.30A1-341[»]
4JV2X-ray2.74A1-341[»]
ProteinModelPortalQ97W02.
SMRQ97W02. Positions 1-348.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-48855N.
STRING273057.SSO2448.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAK42588; AAK42588; SSO2448.
GeneID1453915.
KEGGsso:SSO2448.

Phylogenomic databases

eggNOGCOG0389.
HOGENOMHOG000082707.
KOK04479.
OMADQPISAT.

Enzyme and pathway databases

BioCycSSOL273057:GCH2-2274-MONOMER.

Family and domain databases

Gene3D3.30.1490.100. 1 hit.
HAMAPMF_01113. DNApol_IV.
InterProIPR017961. DNA_pol_Y-fam_little_finger.
IPR001126. DNA_repair_prot_UmuC-like.
IPR017963. DNA_repair_prot_UmuC-like_N.
IPR022880. DNApol_IV.
IPR024728. PolY_HhH_motif.
[Graphical view]
PfamPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
PF11798. IMS_HHH. 1 hit.
[Graphical view]
SUPFAMSSF100879. SSF100879. 1 hit.
PROSITEPS50173. UMUC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ97W02.

Entry information

Entry nameDPO4_SULSO
AccessionPrimary (citable) accession number: Q97W02
Entry history
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: October 1, 2001
Last modified: July 9, 2014
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references