DNAG_HELPY
ID DNAG_HELPY Reviewed; 559 AA.
AC P56064;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=DNA primase {ECO:0000255|HAMAP-Rule:MF_00974};
DE EC=2.7.7.101 {ECO:0000255|HAMAP-Rule:MF_00974};
GN Name=dnaG {ECO:0000255|HAMAP-Rule:MF_00974}; OrderedLocusNames=HP_0012;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.78 ANGSTROMS) OF 413-559.
RX PubMed=23585534; DOI=10.1128/jb.00091-13;
RA Abdul Rehman S.A., Verma V., Mazumder M., Dhar S.K., Gourinath S.;
RT "Crystal structure and mode of helicase binding of the C-terminal domain of
RT primase from Helicobacter pylori.";
RL J. Bacteriol. 195:2826-2838(2013).
CC -!- FUNCTION: RNA polymerase that catalyzes the synthesis of short RNA
CC molecules used as primers for DNA polymerase during DNA replication.
CC {ECO:0000255|HAMAP-Rule:MF_00974}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ssDNA + n NTP = ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate.;
CC EC=2.7.7.101; Evidence={ECO:0000255|HAMAP-Rule:MF_00974};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00974};
CC Note=Binds 1 zinc ion per monomer. {ECO:0000255|HAMAP-Rule:MF_00974};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00974};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_00974};
CC -!- SUBUNIT: Monomer. Interacts with DnaB. {ECO:0000255|HAMAP-
CC Rule:MF_00974}.
CC -!- DOMAIN: Contains an N-terminal zinc-binding domain, a central core
CC domain that contains the primase activity, and a C-terminal DnaB-
CC binding domain. {ECO:0000255|HAMAP-Rule:MF_00974}.
CC -!- SIMILARITY: Belongs to the DnaG primase family. {ECO:0000255|HAMAP-
CC Rule:MF_00974}.
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DR EMBL; AE000511; AAD07082.1; -; Genomic_DNA.
DR PIR; D64521; D64521.
DR RefSeq; NP_206814.1; NC_000915.1.
DR RefSeq; WP_000601638.1; NC_018939.1.
DR PDB; 4EHS; X-ray; 1.78 A; A/B=413-559.
DR PDBsum; 4EHS; -.
DR AlphaFoldDB; P56064; -.
DR SMR; P56064; -.
DR DIP; DIP-3301N; -.
DR IntAct; P56064; 9.
DR MINT; P56064; -.
DR STRING; 85962.C694_00055; -.
DR PaxDb; P56064; -.
DR EnsemblBacteria; AAD07082; AAD07082; HP_0012.
DR KEGG; hpy:HP_0012; -.
DR PATRIC; fig|85962.47.peg.11; -.
DR eggNOG; COG0358; Bacteria.
DR OMA; LMWPIRD; -.
DR PhylomeDB; P56064; -.
DR BRENDA; 2.7.7.101; 2604.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0000428; C:DNA-directed RNA polymerase complex; IEA:UniProtKB-KW.
DR GO; GO:1990077; C:primosome complex; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003896; F:DNA primase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006269; P:DNA replication, synthesis of RNA primer; IBA:GO_Central.
DR CDD; cd03364; TOPRIM_DnaG_primases; 1.
DR Gene3D; 1.10.860.10; -; 1.
DR Gene3D; 3.90.580.10; -; 1.
DR Gene3D; 3.90.980.10; -; 1.
DR HAMAP; MF_00974; DNA_primase_DnaG; 1.
DR InterPro; IPR016136; DNA_helicase_N/primase_C.
DR InterPro; IPR013264; DNA_primase_core_N.
DR InterPro; IPR037068; DNA_primase_core_N_sf.
DR InterPro; IPR006295; DNA_primase_DnaG.
DR InterPro; IPR036977; DNA_primase_Znf_CHC2.
DR InterPro; IPR030846; DnaG_bac.
DR InterPro; IPR031988; DnaG_HBD.
DR InterPro; IPR034151; TOPRIM_DnaG_bac.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR002694; Znf_CHC2.
DR Pfam; PF16730; DnaGprimase_HBD; 1.
DR Pfam; PF13662; Toprim_4; 1.
DR Pfam; PF08275; Toprim_N; 1.
DR Pfam; PF01807; zf-CHC2; 1.
DR PIRSF; PIRSF002811; DnaG; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SMART; SM00400; ZnF_CHCC; 1.
DR TIGRFAMs; TIGR01391; dnaG; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-binding; DNA-directed RNA polymerase;
KW Magnesium; Metal-binding; Nucleotidyltransferase; Primosome;
KW Reference proteome; Transcription; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..559
FT /note="DNA primase"
FT /id="PRO_0000180495"
FT DOMAIN 246..327
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT ZN_FING 37..61
FT /note="CHC2-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT BINDING 298
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT HELIX 442..455
FT /evidence="ECO:0007829|PDB:4EHS"
FT HELIX 457..463
FT /evidence="ECO:0007829|PDB:4EHS"
FT TURN 464..466
FT /evidence="ECO:0007829|PDB:4EHS"
FT HELIX 469..471
FT /evidence="ECO:0007829|PDB:4EHS"
FT HELIX 476..483
FT /evidence="ECO:0007829|PDB:4EHS"
FT HELIX 490..497
FT /evidence="ECO:0007829|PDB:4EHS"
FT HELIX 508..529
FT /evidence="ECO:0007829|PDB:4EHS"
FT HELIX 534..552
FT /evidence="ECO:0007829|PDB:4EHS"
SQ SEQUENCE 559 AA; 63723 MW; E5EB7F2F0BB38170 CRC64;
MILKSSIDRL LQTIDIVEVI SSYVNLRKSG SSYMACCPFH EERSASFSVN QIKGFYHCFG
CGASGDSIKF VMAFEKLSFV EALEKLAHRF NIVLEYDKGV YYDHKEDYHL LEMVSSLYQE
ELFNAPFFLN YLQKRGLSLE SIKAFKLGLC TNRIDYGIEN KGLNKDKLIE LGVLGKSDND
QKTYLRFLDR IMFPIYSPSA QVVGFGGRTL KEKAAKYINS PQSKLFDKSS LLYGYHLAKE
HIYKQKQVIV TEGYLDVILL HQAGFKNAIA TLGTALTPSH LPLLKKGDPE ILLSYDGDKA
GRNAAYKASL MLAKEQRRGG VILFENNLDP ADMIANGQIE TLKNWLSHPM AFIEFVLRRM
ADSYLLDDPL EKDKALKEML GFLKNFSLLL QSEYKPLIAT LLQAPLHVLG IRERVSFQPF
YPKTEKPNRP QRFAHVSSAP SLEFLEKLVI RYLLEDRSLL DLAVGYIHSG VFLHKKQEFD
ALCQEKLDDP KLVALLLDAN LPLKKGGFEK ELRLLILRYF ERQLKEIPKS SLPFSEKMIC
LKKARQAIMK LKQGELVAI
