O73954 (TOP1_PYRFU) 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

Cleaved into the following chain:

1. Endonuclease PI-PfuI
   EC=3.1.-.-
   Alternative name(s):
   Pfu topA intein

Gene names

Name:	topA
Ordered Locus Names:	PF0494

Organism

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]

Taxonomic identifier

186497 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus › Pyrococcus furiosus

Protein attributes

Sequence length	1060 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

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 By similarity. HAMAP-Rule MF_00952
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. HAMAP-Rule MF_00952
Cofactor	Magnesium. Binds two Mg2+ per subunit By similarity. HAMAP-Rule MF_00952
Subunit structure	Monomer By similarity. HAMAP-Rule MF_00952
Post-translational modification	This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential. HAMAP-Rule MF_00952
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. HAMAP-Rule MF_00952
Sequence similarities	Belongs to the type IA topoisomerase family. Contains 1 DOD-type homing endonuclease domain. Contains 1 Toprim domain.

Ontologies

Keywords
Biological process	Intron homing
Domain	Repeat Zinc-finger
Ligand	ATP-binding DNA-binding Magnesium Metal-binding Nucleotide-binding Zinc
Molecular function	Endonuclease Hydrolase Isomerase Nuclease Topoisomerase
PTM	Autocatalytic cleavage Protein splicing
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from electronic annotation. Source: InterPro intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro intron homing Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
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 electronic annotation. Source: EC endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW 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 – 314	314	DNA topoisomerase 1, 1st part HAMAP-Rule MF_00952		PRO_0000034794
	Chain	315 – 687	373	Endonuclease PI-PfuI Potential		PRO_0000034795
	Chain	688 – 1060	373	DNA topoisomerase 1, 2nd part HAMAP-Rule MF_00952		PRO_0000034796
Regions
	Domain	1 – 141	141	Toprim
	Domain	482 – 591	110	DOD-type homing endonuclease
	Zinc finger	978 – 1006	29	C4-type 1 HAMAP-Rule MF_00952
	Zinc finger	1025 – 1050	26	C4-type 2; atypical HAMAP-Rule MF_00952
	Region	196 – 201	6	Interaction with DNA By similarity
Sites
	Active site	690	1	O-(5'-phospho-DNA)-tyrosine intermediate By similarity
	Metal binding	7	1	Magnesium 1; catalytic By similarity
	Metal binding	107	1	Magnesium 1; catalytic By similarity
	Metal binding	107	1	Magnesium 2 By similarity
	Metal binding	109	1	Magnesium 2 By similarity
	Site	52	1	Interaction with DNA By similarity
	Site	166	1	Interaction with DNA By similarity
	Site	170	1	Interaction with DNA By similarity
	Site	692	1	Interaction with DNA By similarity
	Site	880	1	Interaction with DNA By similarity
Experimental info
	Sequence conflict	218	1	F → L in AAC26106. Ref.2
	Sequence conflict	235	1	K → E in AAC26106. Ref.2
	Sequence conflict	293	1	S → P in AAC26106. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	O73954 [UniParc]. Last modified September 26, 2001. Version 2. Checksum: 81D815333D51C0BC	FASTA	1,060	121,182
	10 20 30 40 50 60 MILVIAEKPN VARKIAMALA EVKPIKKTLF GVPYYELIRD GKRLIVASAV GHLYGLAPKN 70 80 90 100 110 120 DFFGYPIFDV EWVPVYIAEK GKEYAKDYIK LLSVLSKRVR EFIVACDYDT EGEVIGYTAL 130 140 150 160 170 180 KYACGVDPGV AKRMKFSALT KRDLIKAWYN LEPTINFGMA NAGIARHILD WYWGVNLSRA 190 200 210 220 230 240 LTHAIKRASG KWVVLSTGRV QGPTLKFLVD REREIQSFVP QPYWVIKLIF EKNGKKYTAN 250 260 270 280 290 300 YEKDKIWDEN EAKRIVLEVK KAPARVTNIE VKQQNRNPPV PFDLGTLQRE AYSAFGFSPK 310 320 330 340 350 360 KTLDIAQSLY EKGFCLHPDT LILTSQGVRK IKELSREGEV FALDFNLKLS KAKYRLLERD 370 380 390 400 410 420 ADEQMYKVTL LDGTELYLTA DHPVLVYREG NLAFVPADKL RETDHVVLVL NKSARDNYGF 430 440 450 460 470 480 LDLLLEITDS QEDYAILENG ETLSLHSLKM LVERGEIKDI AVVGFSHNNF GKVMLRDELW 490 500 510 520 530 540 YLIGYLAGKG GEIKGNGVVI SSRTKEIVGL TKSLNIDLIE TEEGIVLSNK SFVRLLHLIH 550 560 570 580 590 600 YTPRVPEVYG IINNTEWLKA FLAGYYDATL LEGLTLEALY KIKVYLQLLG IRAKIEDNKL 610 620 630 640 650 660 KVHLEDLQRF RELLGKFSRR KLYVETSQVP VFTDFDERSY DFPRILGGDI YIIGIKSIEK 670 680 690 700 710 720 FHYKGKVYDL VVENYHNFIA NGIAVHNCSY PRTESQKLPK NLNYKFIIQN LARIPEYRPY 730 740 750 760 770 780 AHLLLGMPEL KPVEGKKEDP AHPAIYPTGE IPRPGDLTKD EALLYDMIVR RFLAVFMEPA 790 800 810 820 830 840 VRETVKVTIS AGKHKFFISG GRTVKEGWLR VYGKYVKFDE VTLPTFFIGE RIKVLQVKRE 850 860 870 880 890 900 KKKTKPPARY SPAAVIKKME DLGLGTKATR AQILETLYQR GYIEGKKSIK VTPLGMKVIE 910 920 930 940 950 960 TLEKYVPEII SVELTREFEK KMELIMEGKL TKEEVIEEAK IRLTKILEEF KKKELEIGLE 970 980 990 1000 1010 1020 LAKIVVGEEK PPLIVGKCPK CGGDLIVKYN EKTGKRFVGC SNWPKCNVTY PILQRGEIIP 1030 1040 1050 1060 TNKTCCNGAP VVIIREKDGR EWEICLDMNC KEYNTIKKKR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences." Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T. Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]	"A topA intein in Pyrococcus furiosus and its relatedness to the r-gyr intein of Methanococcus jannaschii." Chute I.C., Hu Z., Liu X.-Q. Gene 210:85-92(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 127-1060.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE009950 Genomic DNA. Translation: AAL80618.1. AF042825 Genomic DNA. Translation: AAC26106.1.
RefSeq	NP_578223.1. NC_003413.1.
3D structure databases
ProteinModelPortal	O73954.
ModBase	Search...
Protein-protein interaction databases
STRING	186497.PF0494.
Proteomic databases
PRIDE	O73954.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAL80618; AAL80618; PF0494.
GeneID	1468335.
KEGG	pfu:PF0494.
Phylogenomic databases
eggNOG	COG0551.
HOGENOM	HOG000004019.
KO	K03168.
OMA	LFELLGC.
ProtClustDB	CLSK253381.
Family and domain databases
Gene3D	1.10.290.10. 1 hit. 1.10.460.10. 2 hits. 2.70.20.10. 2 hits. 3.40.50.140. 1 hit.
HAMAP	MF_00952. Topoisom_1_prok.
InterPro	IPR003586. Hint_dom_C. IPR003587. Hint_dom_N. IPR006142. INTEIN. IPR004042. Intein_endonuc. IPR006141. Intein_splice_site. IPR000380. Topo_IA. IPR003601. Topo_IA_2. IPR013497. Topo_IA_cen. IPR013824. Topo_IA_cen_sub1. IPR013825. Topo_IA_cen_sub2. IPR013826. Topo_IA_cen_sub3. IPR023405. Topo_IA_core_domain. IPR003602. Topo_IA_DNA-bd. IPR013498. Topo_IA_Znf. IPR005739. TopoI_arch. IPR006171. Toprim_domain. [Graphical view]
PANTHER	PTHR11390. PTHR11390. 1 hit.
Pfam	PF01131. Topoisom_bac. 2 hits. PF01751. Toprim. 1 hit. PF01396. zf-C4_Topoisom. 1 hit. [Graphical view]
PRINTS	PR00379. INTEIN. PR00417. PRTPISMRASEI.
SMART	SM00305. HintC. 1 hit. SM00306. HintN. 1 hit. SM00437. TOP1Ac. 1 hit. SM00436. TOP1Bc. 1 hit. SM00493. TOPRIM. 1 hit. [Graphical view]
SUPFAM	SSF56712. Topo_IA_core. 1 hit.
TIGRFAMs	TIGR01443. intein_Cterm. 1 hit. TIGR01445. intein_Nterm. 1 hit. TIGR01057. topA_arch. 2 hits.
PROSITE	PS50818. INTEIN_C_TER. 1 hit. PS50819. INTEIN_ENDONUCLEASE. 1 hit. PS50817. INTEIN_N_TER. 1 hit. PS50880. TOPRIM. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

TOP1_PYRFU

Accession

Primary (citable) accession number: O73954

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 20, 2001
Last sequence update:	September 26, 2001
Last modified:	May 29, 2013
This is version 108 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program