P0ABS5 (PRIM_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA primase
EC=2.7.7.-

Gene names

Name:	dnaG
Synonyms:	dnaP, parB
Ordered Locus Names:	b3066, JW3038

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	581 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks during chromosomal DNA synthesis.
Cofactor	Binds 1 zinc ion per monomer.
Subunit structure	Monomer.
Sequence similarities	Belongs to the DNA primase family. Contains 1 Toprim domain.
Sequence caution	The sequence CAA23531.1 differs from that shown. Reason: Frameshift at positions 106 and 169.

Ontologies

Keywords
Biological process	DNA replication Transcription
Cellular component	DNA-directed RNA polymerase Primosome
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Cellular_component	cytoplasm Inferred from direct assay PubMed 340457. Source: EcoliWiki replisome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA primase activity Inferred from direct assay PubMed 340457. Source: EcoliWiki zinc ion binding Inferred from direct assay Ref.6. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
dnaB	P0ACB0	2	EBI-549259,EBI-548978

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 581

581

DNA primase

PRO_0000180490

Regions

Domain

259 – 341

83

Toprim

Zinc finger

40 – 64

25

CHC2-type By similarity

Experimental info

Sequence conflict

24

1

D → N in CAA23636. Ref.5

Secondary structure

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581

Helix Strand Turn

Details...

Helix

116 – 131

16

Helix

134 – 136

3

Helix

137 – 145

9

Helix

150 – 156

7

Beta strand

159 – 161

3

Beta strand

163 – 165

3

Helix

167 – 172

6

Helix

176 – 184

9

Beta strand

187 – 190

4

Beta strand

196 – 199

4

Beta strand

202 – 209

8

Beta strand

211 – 213

3

Beta strand

215 – 225

11

Beta strand

229 – 232

4

Turn

241 – 243

3

Helix

248 – 253

6

Beta strand

261 – 266

6

Helix

267 – 275

9

Beta strand

281 – 283

3

Beta strand

285 – 288

4

Helix

291 – 300

10

Beta strand

302 – 311

10

Helix

312 – 325

14

Helix

326 – 328

3

Beta strand

334 – 340

7

Helix

346 – 362

17

Helix

368 – 376

9

Helix

377 – 379

3

Helix

385 – 399

15

Helix

405 – 419

15

Helix

424 – 427

4

Helix

448 – 460

13

Helix

462 – 467

6

Turn

472 – 474

3

Helix

476 – 478

3

Helix

482 – 493

12

Helix

500 – 505

6

Turn

507 – 509

3

Helix

510 – 512

3

Helix

513 – 540

28

Turn

541 – 543

3

Helix

544 – 558

15

Turn

559 – 561

3

Helix

565 – 577

13

Sequences

	Sequence		Length	Mass (Da)
	P0ABS5 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 294CF020E7B45D94	FASTA	581	65,565
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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]	"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: ZINC-BINDING.
[7]	"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.
[8]	"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.
+	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.

PIR

RYEC2. A03423.

RefSeq

NP_417538.1. NC_000913.2.
YP_491258.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P0ABS5.

SMR

P0ABS5. Positions 4-418, 447-581.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-47954N.

IntAct

P0ABS5. 14 interactions.

MINT

MINT-1222307.

STRING

511145.b3066.

Proteomic databases

PaxDb

P0ABS5.

PRIDE

P0ABS5.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76102; AAC76102; b3066.
BAE77117; BAE77117; BAE77117.

GeneID

12933152.
947570.

KEGG

ecj:Y75_p2992.
eco:b3066.

PATRIC

32121546. VBIEscCol129921_3160.

Organism-specific databases

EchoBASE

EB0235.

EcoGene

EG10239. dnaG.

Phylogenomic databases

eggNOG

COG0358.

HOGENOM

HOG000014483.

KO

K02316.

OMA

HMFDSML.

ProtClustDB

PRK05667.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P0ABS5.

Family and domain databases

Gene3D

1.10.860.10. 1 hit.
3.90.580.10. 1 hit.
3.90.980.10. 1 hit.

InterPro

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]

Pfam

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]

PIRSF

PIRSF002811. DnaG. 1 hit.

SMART

SM00766. DnaG_DnaB_bind. 1 hit.
SM00493. TOPRIM. 1 hit.
SM00400. ZnF_CHCC. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01391. dnaG. 1 hit.

PROSITE

PS50880. TOPRIM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0ABS5.

Entry information

Entry name

PRIM_ECOLI

Accession

Primary (citable) accession number: P0ABS5
Secondary accession number(s): P02922 , P02923, Q2M9D9, Q47613

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program