DNA polymerase IV - Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

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Q97W02 (DPO4_SULSO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 97. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA polymerase IV
Short name=Pol IV
EC=2.7.7.7

Gene names

Name:	dbh
Synonyms:	dpo4
Ordered Locus Names:	SSO2448

Organism

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) [Reference proteome] [HAMAP]

Taxonomic identifier

273057 [NCBI]

Taxonomic lineage

Archaea › Crenarchaeota › Thermoprotei › Sulfolobales › Sulfolobaceae › Sulfolobus ›

Protein attributes

Sequence length	352 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
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

Keywords
Biological process	DNA damage DNA repair DNA replication
Cellular component	Cytoplasm
Ligand	DNA-binding Magnesium Metal-binding
Molecular function	DNA-directed DNA polymerase Mutator protein Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: HAMAP DNA-dependent DNA replication Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: HAMAP damaged DNA binding Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 352

352

DNA polymerase IV HAMAP-Rule MF_01113

PRO_0000173976

Regions

Domain

3 – 187

185

UmuC

Sites

Active site

106

Metal binding

Magnesium

Metal binding

105

Magnesium

Site

Substrate discrimination

Experimental info

Mutagenesis

105 – 106

DE → AA: Loss of function. Ref.4

Secondary structure

352

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q97W02 [UniParc].

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

352

40,193

        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' referencesShow '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. 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE006641 Genomic DNA. Translation: AAK42588.1.

PIR

E90416.

RefSeq

NP_343798.1. NC_002754.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JX4	X-ray	1.70	A	1-352	[»]
1JXL	X-ray	2.10	A	1-352	[»]
1N48	X-ray	2.20	A	1-352	[»]
1N56	X-ray	2.40	A/B	1-352	[»]
1RYR	X-ray	2.28	A	1-352	[»]
1RYS	X-ray	2.03	A/B	1-352	[»]
1S0M	X-ray	2.70	A/B	1-352	[»]
1S0N	X-ray	2.80	A	1-352	[»]
1S0O	X-ray	2.10	A/B	1-352	[»]
1S10	X-ray	2.10	A	1-352	[»]
1S97	X-ray	2.40	A/B/C/D	1-352	[»]
1S9F	X-ray	2.00	A/B/C/D	1-352	[»]
2AGO	X-ray	2.85	A	1-341	[»]
2AGP	X-ray	2.90	A/B	1-341	[»]
2AGQ	X-ray	2.10	A	1-341	[»]
2ASD	X-ray	1.95	A/B	2-352	[»]
2ASJ	X-ray	2.35	A/B	2-352	[»]
2ASL	X-ray	2.65	A/B	2-352	[»]
2ATL	X-ray	2.80	A/B	2-352	[»]
2AU0	X-ray	2.70	A/B	2-352	[»]
2BQ3	X-ray	2.00	A	1-352	[»]
2BQR	X-ray	2.37	A	1-352	[»]
2BQU	X-ray	2.50	A	1-352	[»]
2BR0	X-ray	2.17	A	1-352	[»]
2C22	X-ray	2.56	A	1-352	[»]
2C28	X-ray	2.27	A	1-352	[»]
2C2D	X-ray	2.57	A	1-352	[»]
2C2E	X-ray	2.61	A	1-352	[»]
2C2R	X-ray	2.55	A	1-352	[»]
2IA6	X-ray	2.50	A/B	1-352	[»]
2IBK	X-ray	2.25	A	1-352	[»]
2IMW	X-ray	2.05	P	1-348	[»]
2J6S	X-ray	2.50	A	1-352	[»]
2J6T	X-ray	2.60	A	1-352	[»]
2J6U	X-ray	2.50	A	1-352	[»]
2JEF	X-ray	2.17	A	1-352	[»]
2JEG	X-ray	2.38	A	1-352	[»]
2JEI	X-ray	2.39	A	1-352	[»]
2JEJ	X-ray	1.86	A	1-352	[»]
2R8G	X-ray	2.70	A	1-352	[»]
2R8H	X-ray	2.48	A	1-352	[»]
2R8I	X-ray	2.38	A	1-352	[»]
2RDI	X-ray	1.92	A	1-341	[»]
2RDJ	X-ray	2.20	A/B	1-352	[»]
2UVR	X-ray	2.90	A	1-352	[»]
2UVU	X-ray	2.70	A	1-352	[»]
2UVV	X-ray	2.20	A	1-352	[»]
2UVW	X-ray	2.09	A	1-352	[»]
2V4Q	X-ray	2.60	A	1-352	[»]
2V4R	X-ray	2.50	A	1-352	[»]
2V9W	X-ray	3.00	A/B	1-352	[»]
2VA2	X-ray	2.80	A/B	1-352	[»]
2VA3	X-ray	2.98	A	1-352	[»]
2W8K	X-ray	3.10	A	1-352	[»]
2W8L	X-ray	3.00	A	1-352	[»]
2W9A	X-ray	2.60	A	1-352	[»]
2W9B	X-ray	2.28	A/B	1-352	[»]
2W9C	X-ray	2.87	A/B	1-352	[»]
2XC9	X-ray	2.20	A	1-352	[»]
2XCA	X-ray	2.50	A	1-352	[»]
2XCP	X-ray	2.60	A/B	1-352	[»]
3FDS	X-ray	2.05	A	1-352	[»]
3GII	X-ray	2.60	A	2-341	[»]
3GIJ	X-ray	2.40	A/B	2-341	[»]
3GIK	X-ray	2.90	A	2-341	[»]
3GIL	X-ray	2.71	A/B	2-341	[»]
3GIM	X-ray	2.70	A	2-341	[»]
3KHG	X-ray	2.96	A/B	2-341	[»]
3KHH	X-ray	2.70	A/B	2-341	[»]
3KHL	X-ray	2.10	A/B	2-341	[»]
3KHR	X-ray	2.01	A/B	2-341	[»]
3M9M	X-ray	2.90	B	1-352	[»]
3M9N	X-ray	1.93	B	1-352	[»]
3M9O	X-ray	2.00	B	1-352	[»]
3PR4	X-ray	2.65	A	1-341	[»]
3PR5	X-ray	2.40	B	1-341	[»]
3PVX	X-ray	3.03	A	1-341	[»]
3PW0	X-ray	2.91	A	1-341	[»]
3PW2	X-ray	2.74	A	1-341	[»]
3PW4	X-ray	2.90	A	1-341	[»]
3PW5	X-ray	3.00	A	1-341	[»]
3PW7	X-ray	2.90	A/E	1-341	[»]
3QZ7	X-ray	2.00	A	1-352	[»]
3QZ8	X-ray	2.00	A	1-352	[»]
3RAQ	X-ray	2.25	A/B	2-341	[»]
3RAX	X-ray	1.89	A/B	2-341	[»]
3RB0	X-ray	3.22	A/B	2-341	[»]
3RB3	X-ray	2.80	A	2-341	[»]
3RB4	X-ray	2.80	A/B	2-341	[»]
3RB6	X-ray	2.70	A/B	2-341	[»]
3RBD	X-ray	2.50	A/B	2-341	[»]
3RBE	X-ray	2.80	A/B	2-341	[»]
3T5H	X-ray	2.35	A	1-341	[»]
3T5J	X-ray	2.40	A	1-341	[»]
3T5K	X-ray	2.90	A	1-341	[»]
3T5L	X-ray	2.90	A	1-341	[»]
3V6H	X-ray	2.30	A/B	1-342	[»]
3V6J	X-ray	2.30	A/J	1-342	[»]
3V6K	X-ray	3.60	A/J	1-342	[»]
4F4W	X-ray	1.90	A/B	231-352	[»]
4F4X	X-ray	2.05	A	231-352	[»]
4F4Y	X-ray	2.34	A/B	231-247	[»]
4F4Z	X-ray	2.30	A/B	1-246	[»]
4F50	X-ray	2.22	A	248-352	[»]
4GC6	X-ray	2.90	A	1-352	[»]
4GC7	X-ray	2.89	A/B	1-352	[»]

ProteinModelPortal

Q97W02.

SMR

Q97W02. Positions 1-348.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48855N.

STRING

273057.SSO2448.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK42588; AAK42588; SSO2448.

GeneID

1453915.

KEGG

sso:SSO2448.

Phylogenomic databases

eggNOG

COG0389.

HOGENOM

HOG000082707.

K04479.

OMA

LWIFANG.

ProtClustDB

PRK01216.

Family and domain databases

Gene3D

3.30.1490.100. 1 hit.

HAMAP

MF_01113. DNApol_IV.

InterPro

IPR017961. 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]

Pfam

PF00817. IMS. 1 hit.
PF11799. IMS_C. 1 hit.
PF11798. IMS_HHH. 1 hit.
[Graphical view]

SUPFAM

SSF100879. DNA_pol_Y-fam_little_finger. 1 hit.

PROSITE

PS50173. UMUC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q97W02.

Entry information

Entry name

DPO4_SULSO

Accession

Primary (citable) accession number: Q97W02

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 2, 2002
Last sequence update:	October 1, 2001
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Family and domain databases

Other

Entry information

Relevant documents