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Protein

DNA primase

Gene

dnaG

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: Annotation score: 3 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.UniRule annotation

Cofactori

Protein has several cofactor binding sites:
  • Zn2+UniRule annotationNote: Binds 1 zinc ion per monomer.UniRule annotation
  • Mg2+UniRule annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi252 – 2521Magnesium 1; catalyticUniRule annotation
Metal bindingi296 – 2961Magnesium 1; catalyticUniRule annotation
Metal bindingi296 – 2961Magnesium 2UniRule annotation
Metal bindingi298 – 2981Magnesium 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri37 – 6125CHC2-typeUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA primase activity Source: InterPro
  3. zinc ion binding Source: InterPro
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

BioCyciHPY:HP0012-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA primaseUniRule annotation (EC:2.7.7.-UniRule annotation)
Gene namesi
Name:dnaGUniRule annotation
Ordered Locus Names:HP_0012
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
ProteomesiUP000000429 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

DNA-directed RNA polymerase, Primosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 559559DNA primasePRO_0000180495Add
BLAST

Proteomic databases

PRIDEiP56064.

Interactioni

Subunit structurei

Monomer. Interacts with DnaB.UniRule annotation

Protein-protein interaction databases

DIPiDIP-3301N.
IntActiP56064. 9 interactions.
MINTiMINT-181460.
STRINGi85962.HP0012.

Structurei

Secondary structure

1
559
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi442 – 45514Combined sources
Helixi457 – 4637Combined sources
Turni464 – 4663Combined sources
Helixi469 – 4713Combined sources
Helixi476 – 4838Combined sources
Helixi490 – 4978Combined sources
Helixi508 – 52922Combined sources
Helixi534 – 55219Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EHSX-ray1.78A/B413-559[»]
ProteinModelPortaliP56064.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini246 – 32782ToprimUniRule annotationAdd
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.UniRule annotation

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri37 – 6125CHC2-typeUniRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0358.
KOiK02316.
OMAiEYDKGAY.
OrthoDBiEOG6XDGTR.

Family and domain databases

Gene3Di3.90.580.10. 1 hit.
3.90.980.10. 1 hit.
HAMAPiMF_00974. DNA_primase_DnaG.
InterProiIPR013264. DNA_primase_core_N.
IPR006295. DNA_primase_DnaG.
IPR030846. DnaG_bac.
IPR006171. Toprim_domain.
IPR002694. Znf_CHC2.
[Graphical view]
PfamiPF13662. Toprim_4. 1 hit.
PF08275. Toprim_N. 1 hit.
PF01807. zf-CHC2. 1 hit.
[Graphical view]
PIRSFiPIRSF002811. DnaG. 1 hit.
SMARTiSM00493. TOPRIM. 1 hit.
SM00400. ZnF_CHCC. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01391. dnaG. 1 hit.
PROSITEiPS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P56064-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILKSSIDRL LQTIDIVEVI SSYVNLRKSG SSYMACCPFH EERSASFSVN
60 70 80 90 100
QIKGFYHCFG CGASGDSIKF VMAFEKLSFV EALEKLAHRF NIVLEYDKGV
110 120 130 140 150
YYDHKEDYHL LEMVSSLYQE ELFNAPFFLN YLQKRGLSLE SIKAFKLGLC
160 170 180 190 200
TNRIDYGIEN KGLNKDKLIE LGVLGKSDND QKTYLRFLDR IMFPIYSPSA
210 220 230 240 250
QVVGFGGRTL KEKAAKYINS PQSKLFDKSS LLYGYHLAKE HIYKQKQVIV
260 270 280 290 300
TEGYLDVILL HQAGFKNAIA TLGTALTPSH LPLLKKGDPE ILLSYDGDKA
310 320 330 340 350
GRNAAYKASL MLAKEQRRGG VILFENNLDP ADMIANGQIE TLKNWLSHPM
360 370 380 390 400
AFIEFVLRRM ADSYLLDDPL EKDKALKEML GFLKNFSLLL QSEYKPLIAT
410 420 430 440 450
LLQAPLHVLG IRERVSFQPF YPKTEKPNRP QRFAHVSSAP SLEFLEKLVI
460 470 480 490 500
RYLLEDRSLL DLAVGYIHSG VFLHKKQEFD ALCQEKLDDP KLVALLLDAN
510 520 530 540 550
LPLKKGGFEK ELRLLILRYF ERQLKEIPKS SLPFSEKMIC LKKARQAIMK

LKQGELVAI
Length:559
Mass (Da):63,723
Last modified:November 1, 1997 - v1
Checksum:iE5EB7F2F0BB38170
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07082.1.
PIRiD64521.
RefSeqiNP_206814.1. NC_000915.1.
YP_006933935.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD07082; AAD07082; HP_0012.
GeneIDi899091.
KEGGiheo:C694_00055.
hpy:HP0012.
PATRICi20591217. VBIHelPyl33062_0010.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07082.1.
PIRiD64521.
RefSeqiNP_206814.1. NC_000915.1.
YP_006933935.1. NC_018939.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EHSX-ray1.78A/B413-559[»]
ProteinModelPortaliP56064.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-3301N.
IntActiP56064. 9 interactions.
MINTiMINT-181460.
STRINGi85962.HP0012.

Proteomic databases

PRIDEiP56064.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07082; AAD07082; HP_0012.
GeneIDi899091.
KEGGiheo:C694_00055.
hpy:HP0012.
PATRICi20591217. VBIHelPyl33062_0010.

Phylogenomic databases

eggNOGiCOG0358.
KOiK02316.
OMAiEYDKGAY.
OrthoDBiEOG6XDGTR.

Enzyme and pathway databases

BioCyciHPY:HP0012-MONOMER.

Family and domain databases

Gene3Di3.90.580.10. 1 hit.
3.90.980.10. 1 hit.
HAMAPiMF_00974. DNA_primase_DnaG.
InterProiIPR013264. DNA_primase_core_N.
IPR006295. DNA_primase_DnaG.
IPR030846. DnaG_bac.
IPR006171. Toprim_domain.
IPR002694. Znf_CHC2.
[Graphical view]
PfamiPF13662. Toprim_4. 1 hit.
PF08275. Toprim_N. 1 hit.
PF01807. zf-CHC2. 1 hit.
[Graphical view]
PIRSFiPIRSF002811. DnaG. 1 hit.
SMARTiSM00493. TOPRIM. 1 hit.
SM00400. ZnF_CHCC. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01391. dnaG. 1 hit.
PROSITEiPS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700392 / 26695.
  2. "Crystal structure and mode of helicase binding of the C-terminal domain of primase from Helicobacter pylori."
    Abdul Rehman S.A., Verma V., Mazumder M., Dhar S.K., Gourinath S.
    J. Bacteriol. 195:2826-2838(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) OF 413-559.

Entry informationi

Entry nameiDNAG_HELPY
AccessioniPrimary (citable) accession number: P56064
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: April 29, 2015
This is version 102 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. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  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

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 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.