P14294 (TOP3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase 3
EC=5.99.1.2

Alternative name(s):
DNA topoisomerase III

Gene names

Name:	topB
Ordered Locus Names:	b1763, JW1752

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	653 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Releases the supercoiling and torsional tension of DNA 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 than 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. TOP3 is a potent decatenase.
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Sequence similarities	Belongs to the type IA topoisomerase family. Contains 1 Toprim domain.

Ontologies

Keywords
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA topological change 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 type I activity Inferred from direct assay. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 653

653

DNA topoisomerase 3

PRO_0000145184

Regions

Domain

1 – 135

135

Toprim

Sites

Active site

328

1

O-(5'-phospho-DNA)-tyrosine intermediate By similarity

Secondary structure

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653

Helix Strand Turn

Details...

Beta strand

2 – 8

7

Helix

9 – 16

8

Beta strand

24 – 26

3

Beta strand

29 – 32

4

Turn

33 – 35

3

Beta strand

36 – 40

5

Beta strand

45 – 48

4

Helix

51 – 54

4

Helix

56 – 59

4

Beta strand

75 – 77

3

Helix

79 – 81

3

Helix

82 – 94

13

Beta strand

96 – 101

6

Helix

106 – 118

13

Helix

123 – 127

5

Helix

139 – 146

8

Helix

152 – 155

4

Helix

156 – 185

30

Turn

186 – 188

3

Helix

199 – 214

16

Beta strand

220 – 229

10

Beta strand

235 – 240

6

Helix

244 – 246

3

Turn

247 – 249

3

Helix

259 – 269

11

Beta strand

273 – 275

3

Beta strand

278 – 286

9

Helix

294 – 305

12

Helix

309 – 321

13

Helix

338 – 343

6

Helix

344 – 354

11

Turn

356 – 358

3

Helix

375 – 377

3

Helix

397 – 412

16

Beta strand

418 – 427

10

Beta strand

434 – 436

3

Beta strand

438 – 443

6

Helix

445 – 449

5

Helix

454 – 456

3

Beta strand

472 – 484

13

Helix

493 – 501

9

Helix

503 – 506

4

Helix

510 – 518

9

Beta strand

521 – 523

3

Turn

525 – 527

3

Helix

528 – 537

10

Beta strand

540 – 550

11

Helix

552 – 560

9

Helix

563 – 566

4

Helix

569 – 582

14

Helix

588 – 607

20

Helix

612 – 614

3

Sequences

	Sequence		Length	Mass (Da)
	P14294 [UniParc]. Last modified January 1, 1990. Version 1. Checksum: 301566E14DDDD8C7	FASTA	653	73,217
	10 20 30 40 50 60 MRLFIAEKPS LARAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ PDAYDSRYAR 70 80 90 100 110 120 WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHEASEIVH AGDPDREGQL LVDEVLDYLQ 130 140 150 160 170 180 LAPEKRQQVQ RCLINDLNPQ AVERAIDRLR SNSEFVPLCV SALARARADW LYGINMTRAY 190 200 210 220 230 240 TILGRNAGYQ GVLSVGRVQT PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW 250 260 270 280 290 300 QPSEACEPYQ DEEGRLLHRP LAEHVVNRIS GQPAIVTSYN DKRESESAPL PFSLSALQIE 310 320 330 340 350 360 AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRHAVMNA ISVHAPDLLP 370 380 390 400 410 420 QPVVDPDIRN RCWDDKKVDA HHAIIPTARS SAINLTENEA KVYNLIARQY LMQFCPDAVF 430 440 450 460 470 480 RKCVIELDIA KGKFVAKARF LAEAGWRTLL GSKERDEEND GTPLPVVAKG DELLCEKGEV 490 500 510 520 530 540 VERQTQPPRH FTDATLLSAM TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRGF 550 560 570 580 590 600 LTKKGRYIHS TDAGKALFHS LPEMATRPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY 610 620 630 640 650 QLIDQAKRTP VRQFRGIVAP GSGGSADKKK AAPRKRSAKK SPPADEVGSG AIA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III." Digate R.J., Marians K.J. J. Biol. Chem. 264:17924-17930(1989) [PubMed: 2553698] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20. Strain: HMS-83.
[2]	"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.
[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]	"The structure of Escherichia coli DNA topoisomerase III." Mondragon A., DiGate R. Structure 7:1373-1383(1999) [PubMed: 10574789] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J05076 Genomic DNA. Translation: AAA83923.1.
U00096 Genomic DNA. Translation: AAC74833.1.
AP009048 Genomic DNA. Translation: BAA15551.1.

PIR

JV0049.

RefSeq

NP_416277.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1D6M	X-ray	3.00	A	1-653	[»]
1I7D	X-ray	2.05	A	1-653	[»]
2O19	X-ray	2.45	A/B	1-653	[»]
2O54	X-ray	2.50	A/B	1-653	[»]
2O59	X-ray	2.50	A/B	1-653	[»]
2O5C	X-ray	2.35	A/B	1-653	[»]
2O5E	X-ray	2.50	A/B	1-653	[»]

ProteinModelPortal

P14294.

SMR

P14294. Positions 1-620.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11012N.

IntAct

P14294. 39 interactions.

MINT

MINT-1224249.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000765; EBESCP00000000765; EBESCG00000000638.
EBESCT00000016482; EBESCP00000015773; EBESCG00000015542.

GeneID

946141.

GenomeReviews

Gene locus JW1752 in contig AP009048_GR.
Gene locus b1763 in contig U00096_GR.

KEGG

ecj:JW1752.
eco:b1763.

PATRIC

32118837. VBIEscCol129921_1836.

Organism-specific databases

EchoBASE

EB1007.

EcoGene

EG11014. topB.

Phylogenomic databases

eggNOG

COG0550.

GeneTree

EBGT00050000008919.

HOGENOM

HBG585507.

OMA

TEKTANL.

PhylomeDB

P14294.

ProtClustDB

PRK07726.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11014-MONOMER.
MetaCyc:EG11014-MONOMER.

Gene expression databases

Genevestigator

P14294.

Family and domain databases

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.
IPR005738. TopoIII_bac.
IPR006171. Toprim_domain.
[Graphical view]

Gene3D

G3DSA:1.10.460.10. Topo_IA_cen_sub1. 2 hits.
G3DSA:2.70.20.10. Topo_IA_cen_sub2. 3 hits.

KO

K03169.

PANTHER

PTHR11390. Topo_IA. 1 hit.

Pfam

PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[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

TIGR01056. TopB. 1 hit.

PROSITE

PS00396. TOPOISOMERASE_I_PROK. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

TOP3_ECOLI

Accession

Primary (citable) accession number: P14294

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	January 25, 2012
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program