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Protein

DNA primase/helicase

Gene

4

Organism
Enterobacteria phage T7 (Bacteriophage T7)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Synthesizes short RNA primers for DNA replication. Unwinds the DNA at the replication forks and generates single-stranded DNA for both leading and lagging strand synthesis. The primase synthesizes short RNA primers on the lagging strand that the polymerase elongates using dNTPs.3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Mg2+PROSITE-ProRule annotationNote: Binds two Mg2+ per subunit.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi157 – 1571Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi207 – 2071Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi207 – 2071Magnesium 2PROSITE-ProRule annotation
Metal bindingi209 – 2091Magnesium 2PROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri17 – 3923C4-type; may recognize priming sitesSequence analysisAdd
BLAST
Nucleotide bindingi312 – 3198ATPPROSITE-ProRule annotation

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Transcription

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA primase/helicase (EC:2.7.7.-, EC:3.6.4.12)
Alternative name(s):
Gene product 4
Short name:
Gp4
Gene namesi
Ordered Locus Names:4
OrganismiEnterobacteria phage T7 (Bacteriophage T7)
Taxonomic identifieri10760 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaeAutographivirinaeT7likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000000840 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 566566DNA primase/helicasePRO_0000003355Add
BLAST

Expressioni

Keywords - Developmental stagei

Late protein

Interactioni

Subunit structurei

Homohexamer. Present in a mixture of heptamers and hexamers in the absence of DNA, and assembles onto ssDNA as a hexamer. Interacts with the DNA polymerase gp5; this interaction is essential to initiate leading-strand DNA synthesis. Interacts with single-stranded DNA-binding protein gp2.5.3 Publications

Protein-protein interaction databases

IntActiP03692. 1 interaction.
MINTiMINT-1513747.

Structurei

Secondary structure

1
566
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 155Combined sources
Beta strandi18 – 203Combined sources
Beta strandi26 – 294Combined sources
Beta strandi34 – 363Combined sources
Turni37 – 393Combined sources
Helixi50 – 545Combined sources
Helixi71 – 733Combined sources
Helixi82 – 843Combined sources
Helixi88 – 947Combined sources
Beta strandi96 – 1016Combined sources
Beta strandi104 – 1129Combined sources
Beta strandi118 – 1247Combined sources
Turni126 – 1283Combined sources
Beta strandi131 – 1344Combined sources
Helixi144 – 1463Combined sources
Beta strandi154 – 1585Combined sources
Helixi159 – 16911Combined sources
Turni179 – 1846Combined sources
Helixi185 – 1917Combined sources
Helixi193 – 1964Combined sources
Beta strandi202 – 2054Combined sources
Helixi210 – 22213Combined sources
Turni225 – 2273Combined sources
Beta strandi228 – 2303Combined sources
Beta strandi234 – 2374Combined sources
Helixi238 – 2425Combined sources
Turni243 – 2464Combined sources
Helixi247 – 2548Combined sources
Beta strandi263 – 2675Combined sources
Helixi268 – 2714Combined sources
Helixi272 – 28110Combined sources
Helixi295 – 2995Combined sources
Beta strandi307 – 3137Combined sources
Helixi318 – 33114Combined sources
Beta strandi337 – 3448Combined sources
Helixi346 – 35712Combined sources
Helixi362 – 3643Combined sources
Helixi366 – 37510Combined sources
Helixi377 – 38610Combined sources
Beta strandi387 – 3893Combined sources
Beta strandi391 – 3944Combined sources
Helixi402 – 41413Combined sources
Beta strandi419 – 4268Combined sources
Helixi440 – 45617Combined sources
Beta strandi459 – 4657Combined sources
Beta strandi471 – 4733Combined sources
Helixi475 – 4773Combined sources
Helixi483 – 4853Combined sources
Beta strandi486 – 4916Combined sources
Helixi492 – 4954Combined sources
Beta strandi497 – 5048Combined sources
Beta strandi506 – 5094Combined sources
Beta strandi514 – 5218Combined sources
Turni522 – 5243Combined sources
Beta strandi528 – 5358Combined sources
Turni537 – 5393Combined sources
Beta strandi542 – 5443Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CR0X-ray2.30A271-566[»]
1CR1X-ray2.30A271-566[»]
1CR2X-ray2.30A271-566[»]
1CR4X-ray2.50A271-566[»]
1E0JX-ray3.00A/B/C/D/E/F261-549[»]
1E0KX-ray3.30A/B/C/D/E/F261-549[»]
1NUIX-ray2.90A/B1-255[»]
1Q57X-ray3.45A/B/C/D/E/F/G64-566[»]
ProteinModelPortaliP03692.
SMRiP03692. Positions 10-549.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03692.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini151 – 23888ToprimPROSITE-ProRule annotationAdd
BLAST
Domaini281 – 548268SF4 helicasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 SF4 helicase domain.PROSITE-ProRule annotation
Contains 1 Toprim domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri17 – 3923C4-type; may recognize priming sitesSequence analysisAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

KOiK17680.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR007694. DNA_helicase_DnaB-like_C.
IPR027417. P-loop_NTPase.
IPR013237. Phage_T7_Gp4_N.
IPR006171. Toprim_domain.
IPR027032. Twinkle-like.
[Graphical view]
PANTHERiPTHR12873. PTHR12873. 2 hits.
PfamiPF03796. DnaB_C. 1 hit.
PF08273. Prim_Zn_Ribbon. 1 hit.
[Graphical view]
SMARTiSM00778. Prim_Zn_Ribbon. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51199. SF4_HELICASE. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative initiation. AlignAdd to basket

Isoform Chain a (identifier: P03692-1) [UniParc]FASTAAdd to basket

Also known as: 4a

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MDNSHDSDSV FLYHIPCDNC GSSDGNSLFS DGHTFCYVCE KWTAGNEDTK
60 70 80 90 100
ERASKRKPSG GKPMTYNVWN FGESNGRYSA LTARGISKET CQKAGYWIAK
110 120 130 140 150
VDGVMYQVAD YRDQNGNIVS QKVRDKDKNF KTTGSHKSDA LFGKHLWNGG
160 170 180 190 200
KKIVVTEGEI DMLTVMELQD CKYPVVSLGH GASAAKKTCA ANYEYFDQFE
210 220 230 240 250
QIILMFDMDE AGRKAVEEAA QVLPAGKVRV AVLPCKDANE CHLNGHDREI
260 270 280 290 300
MEQVWNAGPW IPDGVVSALS LRERIREHLS SEESVGLLFS GCTGINDKTL
310 320 330 340 350
GARGGEVIMV TSGSGMGKST FVRQQALQWG TAMGKKVGLA MLEESVEETA
360 370 380 390 400
EDLIGLHNRV RLRQSDSLKR EIIENGKFDQ WFDELFGNDT FHLYDSFAEA
410 420 430 440 450
ETDRLLAKLA YMRSGLGCDV IILDHISIVV SASGESDERK MIDNLMTKLK
460 470 480 490 500
GFAKSTGVVL VVICHLKNPD KGKAHEEGRP VSITDLRGSG ALRQLSDTII
510 520 530 540 550
ALERNQQGDM PNLVLVRILK CRFTGDTGIA GYMEYNKETG WLEPSSYSGE
560
EESHSESTDW SNDTDF
Length:566
Mass (Da):62,655
Last modified:July 21, 1986 - v1
Checksum:iC808C3663FEBE5AA
GO
Isoform Chain b (identifier: P03692-2) [UniParc]FASTAAdd to basket

Also known as: 4b

The sequence of this isoform differs from the canonical sequence as follows:
     1-63: Missing.

Note: No experimental confirmation available. The alternative initiation site Met-64 is uncertain.
Show »
Length:503
Mass (Da):55,743
Checksum:i402AD68B32328F71
GO

Sequence cautioni

The sequence CAA24407.1 differs from that shown. Reason: Erroneous initiation. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 6363Missing in isoform Chain b. CuratedVSP_018683Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01127 Genomic DNA. Translation: CAA24348.1.
V01146 Genomic DNA. Translation: CAA24405.1.
V01146 Genomic DNA. Translation: CAA24407.1. Different initiation.
PIRiA04314. YDBPA7.
RefSeqiNP_041975.1. NC_001604.1. [P03692-1]
NP_041977.1. NC_001604.1. [P03692-2]

Genome annotation databases

GeneIDi1261046.
1261048.
KEGGivg:1261046.
vg:1261048.

Keywords - Coding sequence diversityi

Alternative initiation

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01127 Genomic DNA. Translation: CAA24348.1.
V01146 Genomic DNA. Translation: CAA24405.1.
V01146 Genomic DNA. Translation: CAA24407.1. Different initiation.
PIRiA04314. YDBPA7.
RefSeqiNP_041975.1. NC_001604.1. [P03692-1]
NP_041977.1. NC_001604.1. [P03692-2]

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CR0X-ray2.30A271-566[»]
1CR1X-ray2.30A271-566[»]
1CR2X-ray2.30A271-566[»]
1CR4X-ray2.50A271-566[»]
1E0JX-ray3.00A/B/C/D/E/F261-549[»]
1E0KX-ray3.30A/B/C/D/E/F261-549[»]
1NUIX-ray2.90A/B1-255[»]
1Q57X-ray3.45A/B/C/D/E/F/G64-566[»]
ProteinModelPortaliP03692.
SMRiP03692. Positions 10-549.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP03692. 1 interaction.
MINTiMINT-1513747.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1261046.
1261048.
KEGGivg:1261046.
vg:1261048.

Phylogenomic databases

KOiK17680.

Miscellaneous databases

EvolutionaryTraceiP03692.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR007694. DNA_helicase_DnaB-like_C.
IPR027417. P-loop_NTPase.
IPR013237. Phage_T7_Gp4_N.
IPR006171. Toprim_domain.
IPR027032. Twinkle-like.
[Graphical view]
PANTHERiPTHR12873. PTHR12873. 2 hits.
PfamiPF03796. DnaB_C. 1 hit.
PF08273. Prim_Zn_Ribbon. 1 hit.
[Graphical view]
SMARTiSM00778. Prim_Zn_Ribbon. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
PROSITEiPS51199. SF4_HELICASE. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements."
    Dunn J.J., Studier F.W.
    J. Mol. Biol. 166:477-535(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "Nucleotide sequence from the genetic left end of bacteriophage T7 DNA to the beginning of gene 4."
    Dunn J.J., Studier F.W.
    J. Mol. Biol. 148:303-330(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-179.
  3. "Characterization and crystallization of the helicase domain of bacteriophage T7 gene 4 protein."
    Bird L.E., Haekansson K., Pan H., Wigley D.B.
    Nucleic Acids Res. 25:2620-2626(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  4. "Interactions of gene 2.5 protein and DNA polymerase of bacteriophage T7."
    Kim Y.T., Tabor S., Churchich J.E., Richardson C.C.
    J. Biol. Chem. 267:15032-15040(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PROTEIN GP2.5.
  5. "Gene 4 helicase of bacteriophage T7 mediates strand transfer through pyrimidine dimers, mismatches, and nonhomologous regions."
    Kong D., Griffith J.D., Richardson C.C.
    Proc. Natl. Acad. Sci. U.S.A. 94:2987-2992(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Oligomeric states of bacteriophage T7 gene 4 primase/helicase."
    Crampton D.J., Ohi M., Qimron U., Walz T., Richardson C.C.
    J. Mol. Biol. 360:667-677(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  7. "Helicase-DNA polymerase interaction is critical to initiate leading-strand DNA synthesis."
    Zhang H., Lee S.J., Zhu B., Tran N.Q., Tabor S., Richardson C.C.
    Proc. Natl. Acad. Sci. U.S.A. 108:9372-9377(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "An interaction between DNA polymerase and helicase is essential for the high processivity of the bacteriophage T7 replisome."
    Kulczyk A.W., Akabayov B., Lee S.J., Bostina M., Berkowitz S.A., Richardson C.C.
    J. Biol. Chem. 287:39050-39060(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH PROTEIN GP5.
  9. "Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7."
    Sawaya M.R., Guo S., Tabor S., Richardson C.C., Ellenberger T.
    Cell 99:167-177(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 271-566.
  10. "Crystal structure of T7 gene 4 ring helicase indicates a mechanism for sequential hydrolysis of nucleotides."
    Singleton M.R., Sawaya M.R., Ellenberger T., Wigley D.B.
    Cell 101:589-600(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 261-549.

Entry informationi

Entry nameiPRIM_BPT7
AccessioniPrimary (citable) accession number: P03692
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: May 11, 2016
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral 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.