Reviewed, UniProtKB/Swiss-Prot P06612 (TOP1_ECOLI)

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
    Untwisting enzyme
    Swivelase

Gene names

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

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	865 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	The reaction catalyzed by topoisomerases leads to the conversion of one topological isomer of DNA to another.
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subunit structure	Monomer.
Miscellaneous	When a topoisomerase transiently breaks a DNA backbone bond, it simultaneously forms a protein-DNA link, in which a tyrosyl oxygen in the enzyme is joined to a DNA phosphorus at one end of the enzyme-severed DNA strand.
Sequence similarities	Belongs to the prokaryotic type I/III topoisomerase family.

Ontologies

Keywords
Domain	Repeat Zinc-finger
Ligand	ATP-binding DNA-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA topological change Inferred from electronic annotation. Source: InterPro DNA unwinding during replication Inferred from electronic annotation. Source: InterPro
Cellular component	chromosome Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: InterPro DNA topoisomerase type I activity Inferred from electronic annotation. Source: EC 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
yigZ	P27862	1	EBI-544172,EBI-561235

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 865

865

DNA topoisomerase 1

PRO_0000145147

Regions

Zinc finger

599 – 630

32

C4-type 1

Zinc finger

662 – 689

28

C4-type 2

Zinc finger

711 – 736

26

C4-type 3

Sites

Active site

319

1

For DNA cleavage activity

Experimental info

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 – 17

7

Helix

18 – 20

3

Beta strand

25 – 29

5

Beta strand

34 – 36

3

Helix

67 – 71

5

Turn

75 – 79

5

Turn

87 – 89

3

Helix

90 – 100

11

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

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

361 – 363

3

Helix

377 – 379

3

Helix

385 – 400

16

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

Turn

535 – 538

4

Helix

540 – 554

15

Helix

560 – 571

12

Helix

573 – 578

6

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)
	P06612-1 [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: 3029379] [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: 9097039] [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: 9278503] [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: 16738553] [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: 3032952] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 698-865.
[7]	"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: 8114910] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-590.
[8]	"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: 7779808] [Abstract] Cited for: STRUCTURE BY NMR OF 745-865.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

AP_001900.1.
NP_415790.1.

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:11011N.

IntAct

P06612. 59 interactions.

2-D gel databases

ECO2DBASE

I115.0. 6TH EDITION.

Genome annotation databases

GeneID

945862.

GenomeReviews

Gene locus JW1266 in contig AP009048_GR.
Gene locus b1274 in contig U00096_GR.

KEGG

ecj:JW1266.
eco:b1274.

Organism-specific databases

EchoBASE

EB1006.

EcoGene

EG11013. topA.

CMR

Search...

Phylogenomic databases

HOGENOM

P06612.

OMA

P06612. RKFYGCS.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11013-MON.

Family and domain databases

InterPro

IPR003601. Topo_IA_2.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
IPR000380. Topo_IA_core.
IPR003602. Topo_IA_DNA_bd.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac.
IPR013263. TopoI_Znr_bac.
IPR006171. Toprim_domain.
IPR006154. Toprim_sub.
[Graphical view]

Gene3D

G3DSA:1.10.460.10. Topo_IA_cen_sub1. 2 hits.
G3DSA:1.10.290.10. Topo_IA_cen_sub3. 1 hit.

PANTHER

PTHR11390. Topo_IA. 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]

TIGRFAMs

TIGR01051. topA_bact. 1 hit.

PROSITE

PS00396. TOPOISOMERASE_I_PROK. 1 hit.
[Graphical view]

ProtoNet

Search...

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:	June 16, 2009
This is version 101 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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