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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)DescriptionActionsGraphical viewLength
Metal bindingi157Magnesium 1; catalyticPROSITE-ProRule annotation1
Metal bindingi207Magnesium 1; catalyticPROSITE-ProRule annotation1
Metal bindingi207Magnesium 2PROSITE-ProRule annotation1
Metal bindingi209Magnesium 2PROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri17 – 39C4-type; may recognize priming sitesSequence analysisAdd BLAST23
Nucleotide bindingi312 – 319ATPPROSITE-ProRule annotation8

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

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000033551 – 566DNA primase/helicaseAdd BLAST566

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 interactor.
MINTiMINT-1513747.

Structurei

Secondary structure

1566
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi11 – 15Combined sources5
Beta strandi18 – 20Combined sources3
Beta strandi26 – 29Combined sources4
Beta strandi34 – 36Combined sources3
Turni37 – 39Combined sources3
Helixi50 – 54Combined sources5
Helixi71 – 73Combined sources3
Helixi82 – 84Combined sources3
Helixi88 – 94Combined sources7
Beta strandi96 – 101Combined sources6
Beta strandi104 – 112Combined sources9
Beta strandi118 – 124Combined sources7
Turni126 – 128Combined sources3
Beta strandi131 – 134Combined sources4
Helixi144 – 146Combined sources3
Beta strandi154 – 158Combined sources5
Helixi159 – 169Combined sources11
Turni179 – 184Combined sources6
Helixi185 – 191Combined sources7
Helixi193 – 196Combined sources4
Beta strandi202 – 205Combined sources4
Helixi210 – 222Combined sources13
Turni225 – 227Combined sources3
Beta strandi228 – 230Combined sources3
Beta strandi234 – 237Combined sources4
Helixi238 – 242Combined sources5
Turni243 – 246Combined sources4
Helixi247 – 254Combined sources8
Beta strandi263 – 267Combined sources5
Helixi268 – 271Combined sources4
Helixi272 – 281Combined sources10
Helixi295 – 299Combined sources5
Beta strandi307 – 313Combined sources7
Helixi318 – 331Combined sources14
Beta strandi337 – 344Combined sources8
Helixi346 – 357Combined sources12
Helixi362 – 364Combined sources3
Helixi366 – 375Combined sources10
Helixi377 – 386Combined sources10
Beta strandi387 – 389Combined sources3
Beta strandi391 – 394Combined sources4
Helixi402 – 414Combined sources13
Beta strandi419 – 426Combined sources8
Helixi440 – 456Combined sources17
Beta strandi459 – 465Combined sources7
Beta strandi471 – 473Combined sources3
Helixi475 – 477Combined sources3
Helixi483 – 485Combined sources3
Beta strandi486 – 491Combined sources6
Helixi492 – 495Combined sources4
Beta strandi497 – 504Combined sources8
Beta strandi506 – 509Combined sources4
Beta strandi514 – 521Combined sources8
Turni522 – 524Combined sources3
Beta strandi528 – 535Combined sources8
Turni537 – 539Combined sources3
Beta strandi542 – 544Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03692.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini151 – 238ToprimPROSITE-ProRule annotationAdd BLAST88
Domaini281 – 548SF4 helicasePROSITE-ProRule annotationAdd BLAST268

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri17 – 39C4-type; may recognize priming sitesSequence analysisAdd BLAST23

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 differs from that shown. Reason: Erroneous initiation.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0186831 – 63Missing in isoform Chain b. CuratedAdd BLAST63

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP03692. 1 interactor.
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...

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: November 30, 2016
This is version 135 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.