P06612 (TOP1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase 1
EC=5.99.1.2

Alternative name(s):
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme

Gene names

Name:	topA
Synonyms:	supX
Ordered Locus Names:	b1274, JW1266

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	865 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Ref.8 Ref.9 Ref.15
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Ref.8 Ref.9 Ref.14 Ref.15
Cofactor	Magnesium. Binds two Mg2+ ions per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ and Ca2+. Ref.9 Ref.15
Subunit structure	Monomer.
Sequence similarities	Belongs to the type IA topoisomerase family. Contains 1 Toprim domain.

Ontologies

Keywords
Domain	Repeat Zinc-finger
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding Zinc
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA strand elongation Inferred from mutant phenotype PubMed 10347233. Source: EcoCyc DNA topological change Inferred from genetic interaction PubMed 10713132. Source: EcoliWiki
Cellular_component	chromosome Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase type I activity Inferred from mutant phenotype PubMed 10347233. Source: EcoCyc DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 865

865

DNA topoisomerase 1 HAMAP-Rule MF_00952

PRO_0000145147

Regions

Domain

3 – 142

140

Toprim

Zinc finger

599 – 630

32

C4-type 1 HAMAP-Rule MF_00952

Zinc finger

662 – 689

28

C4-type 2 HAMAP-Rule MF_00952

Zinc finger

711 – 736

26

C4-type 3 HAMAP-Rule MF_00952

Region

192 – 197

6

Interaction with DNA HAMAP-Rule MF_00952

Sites

Active site

319

1

O-(5'-phospho-DNA)-tyrosine intermediate Ref.8 Ref.10 Ref.15

Metal binding

9

1

Magnesium 1; catalytic By similarity

Metal binding

111

1

Magnesium 1; catalytic Probable

Metal binding

111

1

Magnesium 2 Probable

Metal binding

113

1

Magnesium 2 Probable

Site

33

1

Interaction with DNA

Site

168

1

Interaction with DNA

Site

169

1

Interaction with DNA

Site

172

1

Interaction with DNA

Site

177

1

Interaction with DNA

Site

184

1

Interaction with DNA

Site

321

1

Interaction with DNA

Site

507

1

Interaction with DNA

Experimental info

Mutagenesis

9

1

E → A: Abolishes enzyme activity. Ref.8

Mutagenesis

9

1

E → Q: No effect on DNA cleavage activity. Ref.8

Mutagenesis

111

1

D → A: Abolishes both magnesium binding and enzyme activity; when associated with A-113 and A-115. Ref.9

Mutagenesis

113

1

D → A: Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-115. Ref.9

Mutagenesis

115

1

E → A: Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-113. Ref.9

Mutagenesis

168

1

R → A: Abolishes enzyme activity. Ref.15

Mutagenesis

172

1

D → A: Abolishes enzyme activity. Ref.15

Mutagenesis

319

1

Y → A: Abolishes enzyme activity. Ref.8

Mutagenesis

321

1

R → A: Abolishes enzyme activity. Ref.8

Mutagenesis

321

1

R → K: No effect. Ref.8

Mutagenesis

365

1

H → A: No effect. Ref.8 Ref.14

Mutagenesis

365

1

H → R: Increases DNA binding affinity. Ref.8 Ref.14

Mutagenesis

496

1

T → A: No effect. Ref.8

Sequence conflict

787

1

P → R in AAA23641. Ref.6

Secondary structure

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865

Helix Strand Turn

Details...

Beta strand

4 – 9

6

Helix

11 – 18

8

Beta strand

25 – 29

5

Beta strand

35 – 37

3

Helix

64 – 71

8

Beta strand

72 – 74

3

Turn

75 – 79

5

Turn

87 – 89

3

Helix

90 – 101

12

Beta strand

104 – 108

5

Helix

114 – 127

14

Helix

131 – 133

3

Beta strand

134 – 136

3

Helix

144 – 152

9

Helix

159 – 186

28

Helix

197 – 213

17

Beta strand

218 – 227

10

Beta strand

229 – 231

3

Beta strand

233 – 241

9

Helix

251 – 263

13

Beta strand

266 – 278

13

Helix

286 – 297

12

Helix

301 – 313

13

Beta strand

316 – 318

3

Helix

329 – 342

14

Helix

345 – 347

3

Beta strand

356 – 358

3

Beta strand

362 – 364

3

Helix

377 – 379

3

Helix

385 – 401

17

Beta strand

406 – 417

12

Beta strand

420 – 431

12

Helix

433 – 437

5

Beta strand

458 – 470

13

Helix

479 – 488

10

Turn

494 – 496

3

Helix

497 – 506

10

Beta strand

509 – 513

5

Beta strand

516 – 519

4

Helix

521 – 533

13

Helix

535 – 538

4

Helix

540 – 554

15

Helix

560 – 579

20

Helix

582 – 584

3

Beta strand

755 – 762

8

Beta strand

764 – 767

4

Beta strand

769 – 773

5

Beta strand

776 – 778

3

Beta strand

780 – 783

4

Turn

784 – 787

4

Helix

797 – 802

6

Turn

803 – 806

4

Helix

812 – 816

5

Beta strand

827 – 832

6

Turn

833 – 836

4

Beta strand

837 – 842

6

Beta strand

853 – 855

3

Sequences

	Sequence		Length	Mass (Da)
	P06612 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: 8C13F767FE5B178C	FASTA	865	97,350
	10 20 30 40 50 60 MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK 70 80 90 100 110 120 KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA 130 140 150 160 170 180 WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS 190 200 210 220 230 240 PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH 250 260 270 280 290 300 QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG 310 320 330 340 350 360 VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN 370 380 390 400 410 420 SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF 430 440 450 460 470 480 RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA 490 500 510 520 530 540 SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY 550 560 570 580 590 600 DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP 610 620 630 640 650 660 TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED AETNALRAKR 670 680 690 700 710 720 RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL 730 740 750 760 770 780 KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF 790 800 810 820 830 840 LAANTFPKSR ETRAPLVEEL YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV 850 860 SSEKDGKATG WSAFYVDGKW VEGKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I." Tse-Dinh Y.-C., Wang J.C. J. Mol. Biol. 191:321-331(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Lynch D.A., Wang J.C. Submitted (SEP-1991) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
[3]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"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.
[5]	"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.
[6]	"DNA sequences of the cysB regions of Salmonella typhimurium and Escherichia coli." Ostrowski J., Jagura-Burdzy G., Kredich N.M. J. Biol. Chem. 262:5999-6005(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 698-865.
[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]	"Identification of active site residues in Escherichia coli DNA topoisomerase I." Chen S.J., Wang J.C. J. Biol. Chem. 273:6050-6056(1998) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLU-9; TYR-319; ARG-321; HIS-365 AND THR-496, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE.
[9]	"The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change." Zhu C.X., Tse-Dinh Y.C. J. Biol. Chem. 275:5318-5322(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASP-111; ASP-113 AND GLU-115, COFACTOR, FUNCTION, ENZYME MECHANISM, METAL-BINDING SITES, CATALYTIC ACTIVITY.
[10]	"Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I." Lima C.D., Wang J.C., Mondragon A. Nature 367:138-146(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-597, PUTATIVE METAL-BINDING SITES, ACTIVE SITE.
[11]	"Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I." Yu L., Zhu C.-X., Tse-Dinh Y.-C., Fesik S.W. Biochemistry 34:7622-7628(1995) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 745-865.
[12]	"Conformational changes in E. coli DNA topoisomerase I." Feinberg H., Lima C.D., Mondragon A. Nat. Struct. Biol. 6:918-922(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 214-477.
[13]	"Protein-nucleotide interactions in E. coli DNA topoisomerase I." Feinberg H., Changela A., Mondragon A. Nat. Struct. Biol. 6:961-968(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 1-597 IN COMPLEXES WITH NUCLEOTIDES.
[14]	"Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA." Perry K., Mondragon A. Structure 11:1349-1358(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 1-592 OF MUTANT ARG-365 IN COMPLEX WITH SINGLE-STANDED DNA, MUTAGENESIS OF HIS-365, CATALYTIC ACTIVITY.
[15]	"Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I." Zhang Z., Cheng B., Tse-Dinh Y.C. Proc. Natl. Acad. Sci. U.S.A. 108:6939-6944(2011) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-596 OF MUTANT ASN-111 IN COMPLEX WITH DNA, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, COFACTOR, MUTAGENESIS OF ARG-168 AND ASP-172, DNA-BINDING SITES, ENZYME MECHANISM.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X04475 Genomic DNA. Translation: CAA28164.1.
M15041 Genomic DNA. Translation: AAA23641.1.
U00096 Genomic DNA. Translation: AAC74356.1.
AP009048 Genomic DNA. Translation: BAA14811.1.

PIR

ISECTP. E64875.

RefSeq

NP_415790.1. NC_000913.2.
YP_489542.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CY0	X-ray	2.45	A	1-597	[»]
1CY1	X-ray	2.30	A	1-597	[»]
1CY2	X-ray	2.30	A	1-597	[»]
1CY4	X-ray	2.55	A	1-597	[»]
1CY6	X-ray	2.50	A	1-597	[»]
1CY7	X-ray	2.40	A	1-597	[»]
1CY8	X-ray	2.45	A	1-597	[»]
1CY9	X-ray	1.80	A/B	214-477	[»]
1CYY	X-ray	2.15	A/B	214-477	[»]
1ECL	X-ray	1.90	A	1-597	[»]
1MW8	X-ray	1.90	X	1-592	[»]
1MW9	X-ray	1.67	X	1-592	[»]
1YUA	NMR	-	A	745-865	[»]
3PWT	X-ray	1.90	A	1-596	[»]
3PX7	X-ray	2.30	A	1-596	[»]

ProteinModelPortal

P06612.

SMR

P06612. Positions 2-619, 745-865.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11011N.

IntAct

P06612. 65 interactions.

MINT

MINT-1218330.

STRING

511145.b1274.

Proteomic databases

PaxDb

P06612.

PRIDE

P06612.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74356; AAC74356; b1274.
BAA14811; BAA14811; BAA14811.

GeneID

12930585.
945862.

KEGG

ecj:Y75_p1248.
eco:b1274.

PATRIC

32117806. VBIEscCol129921_1323.

Organism-specific databases

EchoBASE

EB1006.

EcoGene

EG11013. topA.

Phylogenomic databases

eggNOG

COG0551.

HOGENOM

HOG000004018.

KO

K03168.

OMA

EFWDIHA.

ProtClustDB

PRK07561.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11013-MONOMER.
ECOL316407:JW1266-MONOMER.
MetaCyc:EG11013-MONOMER.

Gene expression databases

Genevestigator

P06612.

Family and domain databases

Gene3D

1.10.460.10. 3 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.

HAMAP

MF_00952. Topoisom_1_prok.

InterPro

IPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR013263. TopoI_Znr_bac.
IPR006171. Toprim_domain.
[Graphical view]

PANTHER

PTHR11390. PTHR11390. 1 hit.

Pfam

PF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]

PRINTS

PR00417. PRTPISMRASEI.

SMART

SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]

SUPFAM

SSF56712. Topo_IA_core. 1 hit.

TIGRFAMs

TIGR01051. topA_bact. 1 hit.

PROSITE

PS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P06612.

Entry information

Entry name

TOP1_ECOLI

Accession

Primary (citable) accession number: P06612

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	February 1, 1995
Last modified:	May 29, 2013
This is version 145 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program