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P0ABS5 (DNAG_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 88. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA primase

EC=2.7.7.-
Gene names
Name:dnaG
Synonyms:dnaP, parB
Ordered Locus Names:b3066, JW3038
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length581 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

RNA polymerase that catalyzes the synthesis of short RNA molecules used as primers for DNA polymerase during DNA replication. Ref.6 Ref.7

Cofactor

Binds 1 zinc ion per monomer. Ref.7 Ref.8

Magnesium. Binds two Mg2+ per subunit By similarity. Ref.7 Ref.8

Enzyme regulation

Activity can be regulated by an intermolecular trans association between the zinc-binding domain and the catalytic core domain of two different primase molecules. Ref.12

Subunit structure

Monomer. Interacts with DnaB. The primase-helicase complex is composed of up to three DnaG bound to one DnaB hexamer. Ref.6 Ref.7 Ref.9 Ref.11 Ref.15 Ref.16

Domain

Contains an N-terminal zinc-binding domain, a central core domain that contains the primase activity, and a C-terminal DnaB-binding domain. Ref.14 Ref.15 Ref.16

Sequence similarities

Belongs to the DnaG primase family.

Contains 1 Toprim domain.

Sequence caution

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

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 581581DNA primase HAMAP-Rule MF_00974
PRO_0000180490

Regions

Domain259 – 34183Toprim
Zinc finger40 – 6425CHC2-type By similarity

Sites

Metal binding2651Magnesium 1; catalytic By similarity
Metal binding3091Magnesium 1; catalytic By similarity
Metal binding3091Magnesium 2 By similarity
Metal binding3111Magnesium 2 By similarity

Experimental info

Mutagenesis1651W → A: Abolishes DNA-binding and primer synthesis. Ref.17
Mutagenesis1991R → A: Abolishes primer synthesis but can still bind DNA. Abolishes DNA-binding; when associated with A-201. Ref.17
Mutagenesis2011R → A: Abolishes primer synthesis but can still bind DNA. Abolishes DNA-binding; when associated with A-199. Ref.17
Mutagenesis5761Q → A: Decreases interaction with DnaB and primase activity. Ref.9
Sequence conflict241D → N in CAA23636. Ref.5

Secondary structure

............................................................................... 581
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0ABS5 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 294CF020E7B45D94

FASTA58165,565
        10         20         30         40         50         60 
MAGRIPRVFI NDLLARTDIV DLIDARVKLK KQGKNFHACC PFHNEKTPSF TVNGEKQFYH 

        70         80         90        100        110        120 
CFGCGAHGNA IDFLMNYDKL EFVETVEELA AMHNLEVPFE AGSGPSQIER HQRQTLYQLM 

       130        140        150        160        170        180 
DGLNTFYQQS LQQPVATSAR QYLEKRGLSH EVIARFAIGF APPGWDNVLK RFGGNPENRQ 

       190        200        210        220        230        240 
SLIDAGMLVT NDQGRSYDRF RERVMFPIRD KRGRVIGFGG RVLGNDTPKY LNSPETDIFH 

       250        260        270        280        290        300 
KGRQLYGLYE AQQDNAEPNR LLVVEGYMDV VALAQYGINY AVASLGTSTT ADHIQLLFRA 

       310        320        330        340        350        360 
TNNVICCYDG DRAGRDAAWR ALETALPYMT DGRQLRFMFL PDGEDPDTLV RKEGKEAFEA 

       370        380        390        400        410        420 
RMEQAMPLSA FLFNSLMPQV DLSTPDGRAR LSTLALPLIS QVPGETLRIY LRQELGNKLG 

       430        440        450        460        470        480 
ILDDSQLERL MPKAAESGVS RPVPQLKRTT MRILIGLLVQ NPELATLVPP LENLDENKLP 

       490        500        510        520        530        540 
GLGLFRELVN TCLSQPGLTT GQLLEHYRGT NNAATLEKLS MWDDIADKNI AEQTFTDSLN 

       550        560        570        580 
HMFDSLLELR QEELIARERT HGLSNEERLE LWTLNQELAK K 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRRYEC2. A03423.
RefSeqNP_417538.1. NC_000913.3.
YP_491258.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP0ABS5.
SMRP0ABS5. Positions 4-418, 447-581.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-47954N.
IntActP0ABS5. 17 interactions.
MINTMINT-1222307.
STRING511145.b3066.

Proteomic databases

PaxDbP0ABS5.
PRIDEP0ABS5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76102; AAC76102; b3066.
BAE77117; BAE77117; BAE77117.
GeneID12933152.
947570.
KEGGecj:Y75_p2992.
eco:b3066.
PATRIC32121546. VBIEscCol129921_3160.

Organism-specific databases

EchoBASEEB0235.
EcoGeneEG10239. dnaG.

Phylogenomic databases

eggNOGCOG0358.
HOGENOMHOG000014483.
KOK02316.
OMAVMDHDQL.
OrthoDBEOG6XDGTR.
PhylomeDBP0ABS5.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0ABS5.

Family and domain databases

Gene3D1.10.860.10. 1 hit.
3.90.580.10. 1 hit.
3.90.980.10. 1 hit.
HAMAPMF_00974. DNA_primase_DnaG.
InterProIPR016136. 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]
PfamPF10410. 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]
PIRSFPIRSF002811. DnaG. 1 hit.
SMARTSM00766. DnaG_DnaB_bind. 1 hit.
SM00493. TOPRIM. 1 hit.
SM00400. ZnF_CHCC. 1 hit.
[Graphical view]
TIGRFAMsTIGR01391. dnaG. 1 hit.
PROSITEPS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0ABS5.
PROP0ABS5.

Entry information

Entry nameDNAG_ECOLI
AccessionPrimary (citable) accession number: P0ABS5
Secondary accession number(s): P02922 expand/collapse secondary AC list , P02923, Q2M9D9, Q47613
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene