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P0ABS5

- DNAG_ECOLI

UniProt

P0ABS5 - DNAG_ECOLI

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Protein
DNA primase
Gene
dnaG, dnaP, parB, b3066, JW3038
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication.2 Publications

Cofactori

Binds 1 zinc ion per monomer.2 Publications
Magnesium. Binds two Mg2+ per subunit By similarity.2 Publications

Enzyme regulationi

Activity can be regulated by an intermolecular trans association between the zinc-binding domain and the catalytic core domain of two different primase molecules.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi265 – 2651Magnesium 1; catalytic By similarity
Metal bindingi309 – 3091Magnesium 1; catalytic By similarity
Metal bindingi309 – 3091Magnesium 2 By similarity
Metal bindingi311 – 3111Magnesium 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri40 – 6425CHC2-type By similarity
Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA primase activity Source: EcoliWiki
  3. protein binding Source: IntAct
  4. zinc ion binding Source: EcoliWiki

GO - Biological processi

  1. DNA replication, synthesis of RNA primer Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Transcription

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10239-MONOMER.
ECOL316407:JW3038-MONOMER.
MetaCyc:EG10239-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA primase (EC:2.7.7.-)
Gene namesi
Name:dnaG
Synonyms:dnaP, parB
Ordered Locus Names:b3066, JW3038
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10239. dnaG.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: EcoliWiki
  2. primosome complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi165 – 1651W → A: Abolishes DNA-binding and primer synthesis. 1 Publication
Mutagenesisi199 – 1991R → A: Abolishes primer synthesis but can still bind DNA. Abolishes DNA-binding; when associated with A-201. 1 Publication
Mutagenesisi201 – 2011R → A: Abolishes primer synthesis but can still bind DNA. Abolishes DNA-binding; when associated with A-199. 1 Publication
Mutagenesisi576 – 5761Q → A: Decreases interaction with DnaB and primase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 581581DNA primaseUniRule annotation
PRO_0000180490Add
BLAST

Proteomic databases

PaxDbiP0ABS5.
PRIDEiP0ABS5.

Expressioni

Gene expression databases

GenevestigatoriP0ABS5.

Interactioni

Subunit structurei

Monomer. Interacts with DnaB. The primase-helicase complex is composed of up to three DnaG bound to one DnaB hexamer.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
dnaBP0ACB03EBI-549259,EBI-548978
ssbP0AGE02EBI-549259,EBI-1118620

Protein-protein interaction databases

DIPiDIP-47954N.
IntActiP0ABS5. 17 interactions.
MINTiMINT-1222307.
STRINGi511145.b3066.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi116 – 13116
Helixi134 – 1363
Helixi137 – 1459
Helixi150 – 1567
Beta strandi159 – 1613
Beta strandi163 – 1653
Helixi167 – 1726
Helixi176 – 1849
Beta strandi187 – 1904
Beta strandi196 – 1994
Beta strandi202 – 2098
Beta strandi211 – 2133
Beta strandi215 – 22511
Beta strandi229 – 2324
Turni241 – 2433
Helixi248 – 2536
Beta strandi261 – 2666
Helixi267 – 2759
Beta strandi281 – 2833
Beta strandi285 – 2884
Helixi291 – 30010
Beta strandi302 – 31110
Helixi312 – 32514
Helixi326 – 3283
Beta strandi334 – 3407
Helixi346 – 36217
Helixi368 – 3769
Helixi377 – 3793
Helixi385 – 39915
Helixi405 – 41915
Helixi424 – 4274
Helixi448 – 46013
Helixi462 – 4676
Turni472 – 4743
Helixi476 – 4783
Helixi482 – 49312
Helixi500 – 5056
Turni507 – 5093
Helixi510 – 5123
Helixi513 – 54028
Turni541 – 5433
Helixi544 – 55815
Turni559 – 5613
Helixi565 – 57713

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DD9X-ray1.60A111-433[»]
1DDEX-ray1.70A111-433[»]
1EQNX-ray2.90A/B/C/D/E111-429[»]
1T3WX-ray2.80A/B434-581[»]
2HAJNMR-A434-581[»]
3B39X-ray2.35A/B111-429[»]
ProteinModelPortaliP0ABS5.
SMRiP0ABS5. Positions 4-418, 447-581.

Miscellaneous databases

EvolutionaryTraceiP0ABS5.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini259 – 34183Toprim
Add
BLAST

Domaini

Contains an N-terminal zinc-binding domain, a central core domain that contains the primase activity, and a C-terminal DnaB-binding domain.3 Publications

Sequence similaritiesi

Belongs to the DnaG primase family.
Contains 1 Toprim domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0358.
HOGENOMiHOG000014483.
KOiK02316.
OMAiVMDHDQL.
OrthoDBiEOG6XDGTR.
PhylomeDBiP0ABS5.

Family and domain databases

Gene3Di1.10.860.10. 1 hit.
3.90.580.10. 1 hit.
3.90.980.10. 1 hit.
HAMAPiMF_00974. DNA_primase_DnaG.
InterProiIPR016136. DNA_helicase_N/primase_C.
IPR013264. DNA_primase_core_N.
IPR019475. DNA_primase_DnaB-bd.
IPR006295. DNA_primase_DnaG.
IPR013173. DNA_primase_DnaG_DnaB-bd_dom.
IPR006171. Toprim_domain.
IPR002694. Znf_CHC2.
[Graphical view]
PfamiPF10410. DnaB_bind. 1 hit.
PF08278. DnaG_DnaB_bind. 1 hit.
PF13662. Toprim_4. 1 hit.
PF08275. Toprim_N. 1 hit.
PF01807. zf-CHC2. 1 hit.
[Graphical view]
PIRSFiPIRSF002811. DnaG. 1 hit.
SMARTiSM00766. DnaG_DnaB_bind. 1 hit.
SM00493. TOPRIM. 1 hit.
SM00400. ZnF_CHCC. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01391. dnaG. 1 hit.
PROSITEiPS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ABS5-1 [UniParc]FASTAAdd to Basket

« Hide

MAGRIPRVFI NDLLARTDIV DLIDARVKLK KQGKNFHACC PFHNEKTPSF    50
TVNGEKQFYH CFGCGAHGNA IDFLMNYDKL EFVETVEELA AMHNLEVPFE 100
AGSGPSQIER HQRQTLYQLM DGLNTFYQQS LQQPVATSAR QYLEKRGLSH 150
EVIARFAIGF APPGWDNVLK RFGGNPENRQ SLIDAGMLVT NDQGRSYDRF 200
RERVMFPIRD KRGRVIGFGG RVLGNDTPKY LNSPETDIFH KGRQLYGLYE 250
AQQDNAEPNR LLVVEGYMDV VALAQYGINY AVASLGTSTT ADHIQLLFRA 300
TNNVICCYDG DRAGRDAAWR ALETALPYMT DGRQLRFMFL PDGEDPDTLV 350
RKEGKEAFEA RMEQAMPLSA FLFNSLMPQV DLSTPDGRAR LSTLALPLIS 400
QVPGETLRIY LRQELGNKLG ILDDSQLERL MPKAAESGVS RPVPQLKRTT 450
MRILIGLLVQ NPELATLVPP LENLDENKLP GLGLFRELVN TCLSQPGLTT 500
GQLLEHYRGT NNAATLEKLS MWDDIADKNI AEQTFTDSLN HMFDSLLELR 550
QEELIARERT HGLSNEERLE LWTLNQELAK K 581
Length:581
Mass (Da):65,565
Last modified:July 21, 1986 - v1
Checksum:i294CF020E7B45D94
GO

Sequence cautioni

The sequence CAA23531.1 differs from that shown. Reason: Frameshift at positions 106 and 169.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti24 – 241D → N in CAA23636. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01687 Genomic DNA. Translation: AAA24600.1.
V00274 Genomic DNA. Translation: CAA23531.1. Frameshift.
U28379 Genomic DNA. Translation: AAA89146.1.
U00096 Genomic DNA. Translation: AAC76102.1.
AP009048 Genomic DNA. Translation: BAE77117.1.
V00346 Genomic DNA. Translation: CAA23636.1.
PIRiA03423. RYEC2.
RefSeqiNP_417538.1. NC_000913.3.
YP_491258.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76102; AAC76102; b3066.
BAE77117; BAE77117; BAE77117.
GeneIDi12933152.
947570.
KEGGiecj:Y75_p2992.
eco:b3066.
PATRICi32121546. VBIEscCol129921_3160.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01687 Genomic DNA. Translation: AAA24600.1 .
V00274 Genomic DNA. Translation: CAA23531.1 . Frameshift.
U28379 Genomic DNA. Translation: AAA89146.1 .
U00096 Genomic DNA. Translation: AAC76102.1 .
AP009048 Genomic DNA. Translation: BAE77117.1 .
V00346 Genomic DNA. Translation: CAA23636.1 .
PIRi A03423. RYEC2.
RefSeqi NP_417538.1. NC_000913.3.
YP_491258.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DD9 X-ray 1.60 A 111-433 [» ]
1DDE X-ray 1.70 A 111-433 [» ]
1EQN X-ray 2.90 A/B/C/D/E 111-429 [» ]
1T3W X-ray 2.80 A/B 434-581 [» ]
2HAJ NMR - A 434-581 [» ]
3B39 X-ray 2.35 A/B 111-429 [» ]
ProteinModelPortali P0ABS5.
SMRi P0ABS5. Positions 4-418, 447-581.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-47954N.
IntActi P0ABS5. 17 interactions.
MINTi MINT-1222307.
STRINGi 511145.b3066.

Proteomic databases

PaxDbi P0ABS5.
PRIDEi P0ABS5.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC76102 ; AAC76102 ; b3066 .
BAE77117 ; BAE77117 ; BAE77117 .
GeneIDi 12933152.
947570.
KEGGi ecj:Y75_p2992.
eco:b3066.
PATRICi 32121546. VBIEscCol129921_3160.

Organism-specific databases

EchoBASEi EB0235.
EcoGenei EG10239. dnaG.

Phylogenomic databases

eggNOGi COG0358.
HOGENOMi HOG000014483.
KOi K02316.
OMAi VMDHDQL.
OrthoDBi EOG6XDGTR.
PhylomeDBi P0ABS5.

Enzyme and pathway databases

BioCyci EcoCyc:EG10239-MONOMER.
ECOL316407:JW3038-MONOMER.
MetaCyc:EG10239-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0ABS5.
PROi P0ABS5.

Gene expression databases

Genevestigatori P0ABS5.

Family and domain databases

Gene3Di 1.10.860.10. 1 hit.
3.90.580.10. 1 hit.
3.90.980.10. 1 hit.
HAMAPi MF_00974. DNA_primase_DnaG.
InterProi IPR016136. DNA_helicase_N/primase_C.
IPR013264. DNA_primase_core_N.
IPR019475. DNA_primase_DnaB-bd.
IPR006295. DNA_primase_DnaG.
IPR013173. DNA_primase_DnaG_DnaB-bd_dom.
IPR006171. Toprim_domain.
IPR002694. Znf_CHC2.
[Graphical view ]
Pfami PF10410. DnaB_bind. 1 hit.
PF08278. DnaG_DnaB_bind. 1 hit.
PF13662. Toprim_4. 1 hit.
PF08275. Toprim_N. 1 hit.
PF01807. zf-CHC2. 1 hit.
[Graphical view ]
PIRSFi PIRSF002811. DnaG. 1 hit.
SMARTi SM00766. DnaG_DnaB_bind. 1 hit.
SM00493. TOPRIM. 1 hit.
SM00400. ZnF_CHCC. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR01391. dnaG. 1 hit.
PROSITEi PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12."
    Burton Z.F., Gross C.A., Watanabe K.K., Burgess R.R.
    Cell 32:335-349(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequences of the Escherichia coli dnaG primase gene and regulation of its expression."
    Smiley B.L., Lupski J.R., Svec P.S., McMacken R., Godson G.N.
    Proc. Natl. Acad. Sci. U.S.A. 79:4550-4554(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12."
    Lupski J.R., Smiley B.L., Godson G.N.
    Mol. Gen. Genet. 189:48-57(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-81.
    Strain: K12.
  6. "Primase, the dnaG protein of Escherichia coli. An enzyme which starts DNA chains."
    Rowen L., Kornberg A.
    J. Biol. Chem. 253:758-764(1978) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  7. "Enriched sources of Escherichia coli replication proteins. The dnaG primase is a zinc metalloprotein."
    Stamford N.P.J., Lilley P.E., Dixon N.E.
    Biochim. Biophys. Acta 1132:17-25(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR, SUBUNIT, ZINC-BINDING.
  8. "The role of zinc and the reactivity of cysteines in Escherichia coli primase."
    Griep M.A., Lokey E.R.
    Biochemistry 35:8260-8267(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR, ZINC-BINDING.
  9. "Direct physical interaction between DnaG primase and DnaB helicase of Escherichia coli is necessary for optimal synthesis of primer RNA."
    Lu Y.B., Ratnakar P.V., Mohanty B.K., Bastia D.
    Proc. Natl. Acad. Sci. U.S.A. 93:12902-12907(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DNAB, MUTAGENESIS OF GLN-576.
  10. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  11. "Mechanism and stoichiometry of interaction of DnaG primase with DnaB helicase of Escherichia coli in RNA primer synthesis."
    Mitkova A.V., Khopde S.M., Biswas S.B.
    J. Biol. Chem. 278:52253-52261(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, INTERACTION WITH DNAB.
  12. "Crosstalk between primase subunits can act to regulate primer synthesis in trans."
    Corn J.E., Pease P.J., Hura G.L., Berger J.M.
    Mol. Cell 20:391-401(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  13. "A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases."
    Podobnik M., McInerney P., O'Donnell M., Kuriyan J.
    J. Mol. Biol. 300:353-362(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 109-429.
  14. "Structure of the RNA polymerase domain of E. coli primase."
    Keck J.L., Roche D.D., Lynch A.S., Berger J.M.
    Science 287:2482-2486(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 111-433, DOMAIN.
  15. "Crystal and solution structures of the helicase-binding domain of Escherichia coli primase."
    Oakley A.J., Loscha K.V., Schaeffer P.M., Liepinsh E., Pintacuda G., Wilce M.C., Otting G., Dixon N.E.
    J. Biol. Chem. 280:11495-11504(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 434-581, INTERACTION WITH DNAB, DOMAIN.
  16. "Monomeric solution structure of the helicase-binding domain of Escherichia coli DnaG primase."
    Su X.C., Schaeffer P.M., Loscha K.V., Gan P.H., Dixon N.E., Otting G.
    FEBS J. 273:4997-5009(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 434-581, SUBUNIT, DOMAIN.
  17. "Identification of a DNA primase template tracking site redefines the geometry of primer synthesis."
    Corn J.E., Pelton J.G., Berger J.M.
    Nat. Struct. Mol. Biol. 15:163-169(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 111-429, DNA-BINDING, MUTAGENESIS OF TRP-165; ARG-199 AND ARG-201.

Entry informationi

Entry nameiDNAG_ECOLI
AccessioniPrimary (citable) accession number: P0ABS5
Secondary accession number(s): P02922
, P02923, Q2M9D9, Q47613
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: June 11, 2014
This is version 88 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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