Reviewed, UniProtKB/Swiss-Prot P0ABS5 (PRIM_ECOLI)

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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	581 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
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
Gene Ontology (GO)
Biological process	DNA replication, synthesis of RNA primer Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	alpha DNA polymerase:primase complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA primase activity Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rplA	P0A7L0	1	EBI-549259,EBI-543771

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 581

581

DNA primase

PRO_0000180490

Regions

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

111 – 114

4

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

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

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

Helix

476 – 478

3

Helix

482 – 493

12

Helix

500 – 505

6

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)
	P0ABS5-1 [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: 6186393] [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: 6750604] [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: 9278503] [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: 16738553] [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: 6222240] [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: 1511009] [Abstract] Cited for: ZINC-BINDING.
[7]	"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: 10873470] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 109-429.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

AP_003616.1.
NP_417538.1.

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0ABS5. 13 interactions.

STRING

P0ABS5.

2-D gel databases

ECO2DBASE

G060.0. 6TH EDITION.

Genome annotation databases

GeneID

947570.

GenomeReviews

Gene locus JW3038 in contig AP009048_GR.
Gene locus b3066 in contig U00096_GR.

KEGG

ecj:JW3038.
eco:b3066.

Organism-specific databases

EchoBASE

EB0235.

EcoGene

EG10239. dnaG.

CMR

Search...

Phylogenomic databases

HOGENOM

P0ABS5.

OMA

DDIADKD

Enzyme and pathway databases

BioCyc

EcoCyc:EG10239-MON.
ECOL168927:B3066-MON.

Gene expression databases

Genevestigator

P0ABS5.

Family and domain databases

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.
IPR006154. Toprim_dom_subgr.
IPR006171. Toprim_domain.
IPR002694. Znf_CHC2.
[Graphical view]

Gene3D

G3DSA:1.10.860.10. DnaB_N. 1 hit.
G3DSA:3.90.980.10. Toprim_N. 1 hit.
G3DSA:3.90.580.10. Znf_CHC2. 1 hit.

Pfam

PF10410. DnaB_bind. 1 hit.
PF08278. DnaG_DnaB_bind. 1 hit.
PF01751. Toprim. 1 hit.
PF08275. Toprim_N. 1 hit.
PF01807. zf-CHC2. 1 hit.
[Graphical view]

SMART

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

TIGRFAMs

TIGR01391. dnaG. 1 hit.

ProtoNet

Search...

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:	November 24, 2009
This is version 43 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)