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Protein

DNA polymerase IV

Gene

dbh

Organism
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

Mg2+Note: Binds 2 magnesium ions per subunit.

Temperature dependencei

Highly active from 35 to 95 degrees Celsius. Thermostable.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi7Magnesium1
Sitei12Substrate discrimination1
Metal bindingi105Magnesium1
Active sitei1061

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Mutator protein, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi2.7.7.7. 6163.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase IV (EC:2.7.7.7)
Short name:
Pol IV
Gene namesi
Name:dbh
Synonyms:dpo4
Ordered Locus Names:SSO2448
OrganismiSulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Taxonomic identifieri273057 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus
Proteomesi
  • UP000001974 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi105 – 106DE → AA: Loss of function. 1 Publication2
Mutagenesisi342 – 352Missing : Almost complete loss of interaction with PCNA. 1 PublicationAdd BLAST11

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001739761 – 352DNA polymerase IVAdd BLAST352

Proteomic databases

PRIDEiQ97W02.

Interactioni

Subunit structurei

Monomer. Interacts with the PCNA heterotrimer via PCNA1.1 Publication

Protein-protein interaction databases

DIPiDIP-48855N.
STRINGi273057.SSO2448.

Structurei

Secondary structure

1352
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi11 – 19Combined sources9
Helixi21 – 23Combined sources3
Beta strandi24 – 26Combined sources3
Beta strandi28 – 32Combined sources5
Beta strandi35 – 37Combined sources3
Turni38 – 40Combined sources3
Beta strandi42 – 46Combined sources5
Helixi48 – 51Combined sources4
Turni52 – 54Combined sources3
Beta strandi57 – 59Combined sources3
Helixi61 – 67Combined sources7
Beta strandi71 – 75Combined sources5
Helixi78 – 93Combined sources16
Beta strandi99 – 103Combined sources5
Beta strandi106 – 110Combined sources5
Turni112 – 114Combined sources3
Beta strandi115 – 117Combined sources3
Helixi118 – 136Combined sources19
Beta strandi140 – 147Combined sources8
Helixi148 – 158Combined sources11
Turni159 – 161Combined sources3
Beta strandi163 – 165Combined sources3
Helixi168 – 177Combined sources10
Helixi180 – 182Combined sources3
Helixi188 – 194Combined sources7
Turni196 – 198Combined sources3
Helixi202 – 206Combined sources5
Helixi212 – 215Combined sources4
Helixi219 – 229Combined sources11
Beta strandi243 – 255Combined sources13
Helixi258 – 276Combined sources19
Beta strandi281 – 290Combined sources10
Turni291 – 293Combined sources3
Beta strandi295 – 301Combined sources7
Helixi308 – 325Combined sources18
Beta strandi330 – 340Combined sources11
Beta strandi343 – 346Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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/B5-143[»]
A/B231-247[»]
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[»]
4QW8X-ray2.29A1-341[»]
4QW9X-ray2.40A1-341[»]
4QWAX-ray2.20A1-341[»]
4QWBX-ray1.80A1-343[»]
4QWCX-ray2.40A/D1-342[»]
4QWDX-ray2.05A1-341[»]
4QWEX-ray2.20A1-341[»]
4RUAX-ray3.07A1-341[»]
4RUCX-ray2.90A1-341[»]
4RZRX-ray2.20A/D1-352[»]
4TQRX-ray1.58A1-342[»]
4TQSX-ray2.06A/B1-352[»]
ProteinModelPortaliQ97W02.
SMRiQ97W02.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ97W02.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 187UmuCAdd BLAST185

Domaini

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.

Sequence similaritiesi

Belongs to the DNA polymerase type-Y family.Curated
Contains 1 umuC domain.Curated

Phylogenomic databases

eggNOGiarCOG04582. Archaea.
COG0389. LUCA.
HOGENOMiHOG000082707.
InParanoidiQ97W02.
KOiK04479.
OMAiKSRTLNH.

Family and domain databases

Gene3Di3.30.1490.100. 1 hit.
HAMAPiMF_01113. DNApol_IV. 1 hit.
InterProiIPR017961. DNA_pol_Y-fam_little_finger.
IPR022880. DNApol_IV.
IPR024728. PolY_HhH_motif.
IPR001126. UmuC.
[Graphical view]
PfamiPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
PF11798. IMS_HHH. 1 hit.
[Graphical view]
SUPFAMiSSF100879. SSF100879. 1 hit.
PROSITEiPS50173. UMUC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q97W02-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVLFVDFDY FYAQVEEVLN PSLKGKPVVV CVFSGRFEDS GAVATANYEA
60 70 80 90 100
RKFGVKAGIP IVEAKKILPN AVYLPMRKEV YQQVSSRIMN LLREYSEKIE
110 120 130 140 150
IASIDEAYLD ISDKVRDYRE AYNLGLEIKN KILEKEKITV TVGISKNKVF
160 170 180 190 200
AKIAADMAKP NGIKVIDDEE VKRLIRELDI ADVPGIGNIT AEKLKKLGIN
210 220 230 240 250
KLVDTLSIEF DKLKGMIGEA KAKYLISLAR DEYNEPIRTR VRKSIGRIVT
260 270 280 290 300
MKRNSRNLEE IKPYLFRAIE ESYYKLDKRI PKAIHVVAVT EDLDIVSRGR
310 320 330 340 350
TFPHGISKET AYSESVKLLQ KILEEDERKI RRIGVRFSKF IEAIGLDKFF

DT
Length:352
Mass (Da):40,193
Last modified:October 1, 2001 - v1
Checksum:iC0B0AD4B3A3E87D0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006641 Genomic DNA. Translation: AAK42588.1.
PIRiE90416.
RefSeqiWP_009993137.1. NC_002754.1.

Genome annotation databases

EnsemblBacteriaiAAK42588; AAK42588; SSO2448.
GeneIDi27428748.
KEGGisso:SSO2448.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006641 Genomic DNA. Translation: AAK42588.1.
PIRiE90416.
RefSeqiWP_009993137.1. NC_002754.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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/B5-143[»]
A/B231-247[»]
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[»]
4QW8X-ray2.29A1-341[»]
4QW9X-ray2.40A1-341[»]
4QWAX-ray2.20A1-341[»]
4QWBX-ray1.80A1-343[»]
4QWCX-ray2.40A/D1-342[»]
4QWDX-ray2.05A1-341[»]
4QWEX-ray2.20A1-341[»]
4RUAX-ray3.07A1-341[»]
4RUCX-ray2.90A1-341[»]
4RZRX-ray2.20A/D1-352[»]
4TQRX-ray1.58A1-342[»]
4TQSX-ray2.06A/B1-352[»]
ProteinModelPortaliQ97W02.
SMRiQ97W02.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48855N.
STRINGi273057.SSO2448.

Proteomic databases

PRIDEiQ97W02.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK42588; AAK42588; SSO2448.
GeneIDi27428748.
KEGGisso:SSO2448.

Phylogenomic databases

eggNOGiarCOG04582. Archaea.
COG0389. LUCA.
HOGENOMiHOG000082707.
InParanoidiQ97W02.
KOiK04479.
OMAiKSRTLNH.

Enzyme and pathway databases

BRENDAi2.7.7.7. 6163.

Miscellaneous databases

EvolutionaryTraceiQ97W02.

Family and domain databases

Gene3Di3.30.1490.100. 1 hit.
HAMAPiMF_01113. DNApol_IV. 1 hit.
InterProiIPR017961. DNA_pol_Y-fam_little_finger.
IPR022880. DNApol_IV.
IPR024728. PolY_HhH_motif.
IPR001126. UmuC.
[Graphical view]
PfamiPF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
PF11798. IMS_HHH. 1 hit.
[Graphical view]
SUPFAMiSSF100879. SSF100879. 1 hit.
PROSITEiPS50173. UMUC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPO4_SULSO
AccessioniPrimary (citable) accession number: Q97W02
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: October 1, 2001
Last modified: November 2, 2016
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.