DNAG_GEOSE
ID DNAG_GEOSE Reviewed; 597 AA.
AC Q9X4D0;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 128.
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};
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CRYSTALLIZATION.
RC STRAIN=ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924;
RX PubMed=10095067; DOI=10.1016/s0167-4781(99)00025-1;
RA Pan H., Bird L.E., Wigley D.B.;
RT "Cloning, expression, and purification of Bacillus stearothermophilus DNA
RT primase and crystallization of the zinc-binding domain.";
RL Biochim. Biophys. Acta 1444:429-433(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.71 ANGSTROMS) OF 1-103 IN COMPLEX WITH ZINC,
RP COFACTOR, AND DOMAIN.
RX PubMed=10745010; DOI=10.1016/s0969-2126(00)00101-5;
RA Pan H., Wigley D.B.;
RT "Structure of the zinc-binding domain of Bacillus stearothermophilus DNA
RT primase.";
RL Structure 8:231-239(2000).
RN [3]
RP STRUCTURE BY NMR OF 453-597, INTERACTION WITH DNAB, AND DOMAIN.
RX PubMed=15837199; DOI=10.1016/j.str.2005.01.022;
RA Syson K., Thirlway J., Hounslow A.M., Soultanas P., Waltho J.P.;
RT "Solution structure of the helicase-interaction domain of the primase DnaG:
RT a model for helicase activation.";
RL Structure 13:609-616(2005).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 455-597 IN COMPLEX WITH DNAB,
RP INTERACTION WITH DNAB, AND DOMAIN.
RX PubMed=17947583; DOI=10.1126/science.1147353;
RA Bailey S., Eliason W.K., Steitz T.A.;
RT "Structure of hexameric DnaB helicase and its complex with a domain of DnaG
RT primase.";
RL Science 318:459-463(2007).
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 ECO:0000269|PubMed:10745010};
CC Note=Binds 1 zinc ion per monomer. {ECO:0000255|HAMAP-Rule:MF_00974,
CC ECO:0000269|PubMed:10745010};
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 (By similarity). Interacts with DnaB.
CC {ECO:0000255|HAMAP-Rule:MF_00974, ECO:0000269|PubMed:10745010,
CC ECO:0000269|PubMed:15837199, ECO:0000269|PubMed:17947583}.
CC -!- INTERACTION:
CC Q9X4D0; Q9X4C9: dnaB; NbExp=7; IntAct=EBI-6403005, EBI-6402993;
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:0000305|PubMed:10745010,
CC ECO:0000305|PubMed:15837199, ECO:0000305|PubMed:17947583}.
CC -!- SIMILARITY: Belongs to the DnaG primase family. {ECO:0000255|HAMAP-
CC Rule:MF_00974}.
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DR EMBL; AF106033; AAD20315.1; -; Genomic_DNA.
DR PDB; 1D0Q; X-ray; 1.71 A; A/B=1-103.
DR PDB; 1Z8S; NMR; -; A=452-597.
DR PDB; 2R6A; X-ray; 2.90 A; C=455-597.
DR PDB; 2R6C; X-ray; 4.00 A; G/H/I=455-597.
DR PDB; 4M4W; X-ray; 6.10 A; G/H/I=455-597.
DR PDBsum; 1D0Q; -.
DR PDBsum; 1Z8S; -.
DR PDBsum; 2R6A; -.
DR PDBsum; 2R6C; -.
DR PDBsum; 4M4W; -.
DR AlphaFoldDB; Q9X4D0; -.
DR BMRB; Q9X4D0; -.
DR SMR; Q9X4D0; -.
DR DIP; DIP-48436N; -.
DR IntAct; Q9X4D0; 2.
DR BRENDA; 2.7.7.101; 623.
DR EvolutionaryTrace; Q9X4D0; -.
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:0005524; F:ATP binding; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003678; F:DNA helicase activity; IEA:InterPro.
DR GO; GO:0003896; F:DNA primase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
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; IPR036185; DNA_heli_DnaB-like_N_sf.
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; IPR019475; DNA_primase_DnaB-bd.
DR InterPro; IPR006295; DNA_primase_DnaG.
DR InterPro; IPR036977; DNA_primase_Znf_CHC2.
DR InterPro; IPR030846; DnaG_bac.
DR InterPro; IPR034151; TOPRIM_DnaG_bac.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR002694; Znf_CHC2.
DR Pfam; PF10410; DnaB_bind; 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 SUPFAM; SSF48024; SSF48024; 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; Transcription;
KW Transferase; Zinc; Zinc-finger.
FT CHAIN 1..597
FT /note="DNA primase"
FT /id="PRO_0000180478"
FT DOMAIN 262..342
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT ZN_FING 40..64
FT /note="CHC2-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT REGION 429..448
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 268
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 311
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 311
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT BINDING 313
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00974"
FT HELIX 7..16
FT /evidence="ECO:0007829|PDB:1D0Q"
FT HELIX 19..23
FT /evidence="ECO:0007829|PDB:1D0Q"
FT TURN 24..26
FT /evidence="ECO:0007829|PDB:1D0Q"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:1D0Q"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:1D0Q"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:1D0Q"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:1D0Q"
FT TURN 54..57
FT /evidence="ECO:0007829|PDB:1D0Q"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:1D0Q"
FT TURN 62..64
FT /evidence="ECO:0007829|PDB:1D0Q"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:1D0Q"
FT HELIX 82..93
FT /evidence="ECO:0007829|PDB:1D0Q"
FT HELIX 98..100
FT /evidence="ECO:0007829|PDB:1D0Q"
FT HELIX 459..471
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 475..484
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 492..505
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 513..516
FT /evidence="ECO:0007829|PDB:2R6A"
FT TURN 517..519
FT /evidence="ECO:0007829|PDB:2R6A"
FT STRAND 522..524
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 525..531
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 542..553
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 555..573
FT /evidence="ECO:0007829|PDB:2R6A"
FT HELIX 577..594
FT /evidence="ECO:0007829|PDB:2R6A"
SQ SEQUENCE 597 AA; 67111 MW; 02FA690CB6798447 CRC64;
MGHRIPEETI EAIRRGVDIV DVIGEYVQLK RQGRNYFGLC PFHGEKTPSF SVSPEKQIFH
CFGCGAGGNA FTFLMDIEGI PFVEAAKRLA AKAGVDLSVY ELDVRGRDDG QTDEAKAMTE
AHALLKRFYH HLLVHTKEGQ AALDYLQARG WTKETIDRFE IGYAPDAPDA AAKLLESHSF
SLPVMEKAGL LTKKEDGRYV GRFRNRIMFP IHDHRGETVG FSGRLLGEGH PKYVNSPETP
VFRKGAILYH FHAARVPIRK RQEALLVEGF ADVISAAQAG IDYAIATMGT SLTEEQARIL
RPCDTITICY DGDRAGIEAA WAAAEQLSAL GCRVKVASLP NGLDPDEYIR VYGGERFAGE
AGCRRPLVAF KMAYLRRGKN LQHEGERLRY IDEALREIGK LSSPVEQDYY LRQLAEEFSL
SLSALHEQLS RSQRERTKPR EAPDGETARP MLAKKLLPAF QNAERLLLAH MMRSRDVALV
VQERIGGRFN IEEHRALAAY IYAFYEEGHE ADPGALISRI PGELQPLASD VSLLLIADDV
SEQELEDYIR HVLNRPKWLM LKVKEQEKTE AERRKDFLTA ARIAKEMIEM KKMLSSS
