Reviewed, UniProtKB/Swiss-Prot O58530 (RGYR_PYRHO)

Names and origin

Protein names

Recommended name:
    Reverse gyrase
Cleaved into the following chain:
    1- Recommended name:
            Pho r-Gyr intein
Including the following 2 domains:
    1- Recommended name:
            Helicase
              EC=3.6.1.-
    2- Recommended name:
            Topoisomerase
              EC=5.99.1.3

Gene names

Name:	rgy
Ordered Locus Names:	PH0800

Organism

Pyrococcus horikoshii [Complete proteome] [HAMAP]

Taxonomic identifier

53953 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	1624 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	Modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. It cleaves transiently a single DNA strand and remains covalently bound to the 5' DNA end through a tyrosine residue. May be involved in rewinding the DNA strands in the regions of the chromosome that have opened up to allow transcription or replication By similarity.
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP MF_01125
Subunit structure	Monomer By similarity.
Domain	Both the DNA unwinding and positive supercoiling activities require the cooperation of both domains. The cooperative action between the helicase-like and the topoisomerase domains is specific. The helicase-like domain probably does not directly unwind DNA but acts more likely by driving ATP-dependent conformational changes within the whole enzyme, functioning more like a protein motor. The "latch" region of the N-terminal domain plays a regulatory role in the enzyme, repressing topoisomerase activity in the absence of ATP and therefore preventing the enzyme from acting as an ATP-independent relaxing enzyme; it also helps to coordinate nucleotide hydrolysis by the ATPase domain with the supercoiling activity of the topoisomerase domain By similarity.
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.
Miscellaneous	This enzyme is the only unique feature of hyperthermophilic bacteria/archaea discovered so far. It appears to be essential for adaptation to life at high temperatures. HAMAP MF_01125
Sequence similarities	In the N-terminal section; belongs to the DEAD box helicase family. DDVD subfamily. In the C-terminal section; belongs to the prokaryotic type I/III topoisomerase family. Contains 1 DOD-type homing endonuclease domain. Contains 1 helicase ATP-binding domain.

Ontologies

Keywords
Domain	Zinc-finger
Ligand	ATP-binding DNA-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Helicase Hydrolase Isomerase Topoisomerase
PTM	Autocatalytic cleavage Protein splicing
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA topological change Inferred from electronic annotation. Source: HAMAP DNA unwinding during replication Inferred from electronic annotation. Source: HAMAP intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro
Cellular component	chromosome Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro DNA topoisomerase (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: HAMAP DNA topoisomerase type I activity Inferred from electronic annotation. Source: InterPro endonuclease activity Inferred from electronic annotation. Source: InterPro zinc 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 – 953	953	Reverse gyrase, 1st part Potential		PRO_0000030356
	Chain	954 – 1363	410	Pho r-Gyr intein Potential		PRO_0000030357
	Chain	1364 – 1624	261	Reverse gyrase, 2nd part Potential		PRO_0000030358
Regions
	Domain	93 – 256	164	Helicase ATP-binding
	Domain	1107 – 1222	116	DOD-type homing endonuclease
	Zinc finger	9 – 30	22	C4-type 1 By similarity
	Nucleotide binding	106 – 113	8	ATP By similarity
	Zinc finger	723 – 742	20	C4-type 2 By similarity
	Region	646 – 1624	979	Topoisomerase I HAMAP MF_01125
	Motif	213 – 216	4	DDVD box HAMAP MF_01125
Sites
	Active site	1366	1	For DNA cleavage activity By similarity
	Binding site	89	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	O58530-1 [UniParc]. Last modified August 1, 1998. Version 1. Checksum: B897F8F42FEB6EF5	FASTA	1,624	187,069
	10 20 30 40 50 60 MKAIYRGMCP NCRGAITDER LSNKNPCEGC LSEPILSEDY NELIVAVRNA LKLRGTLKDW 70 80 90 100 110 120 EELYRLNKEV SEIEELFEKS TGFKFWSAQR TWVKRIIRGK SFSIIAPTGM GKSTFGAFIS 130 140 150 160 170 180 IYFATKGKKS YIVVPTTPLV IQTVKKIESM LEKANVSVRL VYYHGNLRKK EKEEALEKIR 190 200 210 220 230 240 NGDFDILITS SQFLATRFKE LLKDKKFDLI FVDDVDAFLK ASKNIDRSLI MLGFSEEIIG 250 260 270 280 290 300 RAWEVIKLKK QLAKLLQNEK KNEEEIEKLN KEIEKIEDEI EEYKRRNKIG ILIVASATGS 310 320 330 340 350 360 AKGDRIKLYR ELLGFEVGSG RSVLRNIVDT YLLPEKPIEE HVVELLRKLG KGGLIFVPID 370 380 390 400 410 420 KGIEYAEELT DYLKSQGFKV ELVSAKNKKG LELFEKGEID YLVGVATYYG TLVRGLDLPH 430 440 450 460 470 480 LIRFAIFTGV PKFRFSMDLE QPTIYRVLGL MSEILEFLPE EKKSEGEKLY ARLRRLIRNI 490 500 510 520 530 540 PQYELMKIEE ALAEGLELEG FHNHVLEVFK QSVEFLREVL KDEEVIKKIA ENPFLSLKEI 550 560 570 580 590 600 EGKLYIEIPD VRTYIQASGR TSRLFAGGIT KGLSVIIVDD QKVFNGLIRQ MRWRFVEFDI 610 620 630 640 650 660 KKFEEVNLKE VLKEIDRDRE KVKLVIEGKI SEQVKDLVKS ALMIVESPNK ARTIASFFGQ 670 680 690 700 710 720 PSKRKIGDLT AYEVSIGDKM LTILASGGHM FDLVTNEGYH GVLILKNNGK PYFVPVYDTI 730 740 750 760 770 780 KRCRDCGHQF VDWEQKGVCP RCGSRNVHDA LENVKAMREL ALEVDEILIG TDPDTEGEKI 790 800 810 820 830 840 AWDIRNVLAP YAPNIKRIEF HEVTRPAILR AIREARDINE DRVNAQLVRR IEDRWIGFEL 850 860 870 880 890 900 SQKLWEVFEN RNLSAGRVQT PVLGWIVQRY KEFTESETDF LGIILENGIN VTIENAKGEV 910 920 930 940 950 960 REVEVKDVII EEKDVNPLPP YTTDTMLQDA SRFLGFSATK TMQLAQDLFE AGLCVTPDTL 970 980 990 1000 1010 1020 VSLSDGRIIE IREAVENSEE SLLGINGLKP KEAKALKFWE IDWDGPIKVI KLKNGHEIKA 1030 1040 1050 1060 1070 1080 TPDHGLLVMR DGKIGWVSAK NIREGDYVAF IYNLGHRGGK KYTLPQLLKE LGISEYENSS 1090 1100 1110 1120 1130 1140 SQELNNREQE MDSKQISIEL DERFWYIFGV ILGKGTLKGD KVVIFQKDVK PVIEEALPFV 1150 1160 1170 1180 1190 1200 RIFESADHIG FSHLILAEVF RRLGVGEGKL HSLVFGLREE YINAMIAGYF DASGTFLRRA 1210 1220 1230 1240 1250 1260 VLTSKRGDIL RMLSVYLYQI GIVNNLRRDE HAGVWELIIS DLEKFREKIY PYLRIKKSQF 1270 1280 1290 1300 1310 1320 DKVYSISKNE GDFLPVASIF RKLKFRDGFK NRILDEEIPR DEVAKVLEYA EDSPEKEFLN 1330 1340 1350 1360 1370 1380 SLVEARVTWV RVEKIEERHY TGKLYDFTTT TENFISNGIV SHNCTYHRTD SIHVSNTGIE 1390 1400 1410 1420 1430 1440 VAKEYITQEI GEEYFTPRKW GEEGAHEAIR PTRPIDTGRL IQLIRDGIIT IPKNLTRDHF 1450 1460 1470 1480 1490 1500 RLYDLIFRRF MASQMKPAKI LYEKAIISTP FKDVEVEGYI DVLYDGWSKI KSLPLRQIPK 1510 1520 1530 1540 1550 1560 LEKGQRLRVK EVKQWRAPKV SLYTQGDVIA LMKERGIGRP STYAKIVQTL LQRGYVIETK 1570 1580 1590 1600 1610 1620 GKKKLVPTEK GIKVYQYLIT KYKDLVSEER TRQLEKIMDM VEEAKADYQD VLNELYEEIK RYVR

References

[1]

"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3." Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H. DNA Res. 5:55-76(1998) [PubMed: 9679194] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: OT3.

Cross-references

Sequence databases
EMBLGenBankDDBJ	BA000001 Genomic DNA. Translation: BAA29893.1.
PIR	C71129.
RefSeq	NP_142736.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	1443130.
GenomeReviews	Gene locus PH0800 in contig BA000001_GR.
KEGG	pho:PH0800.
NMPDR	fig|70601.1.peg.783.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HBG312311.
OMA	ENRNLSA.
Enzyme and pathway databases
BioCyc	PHOR70601:PH0800-MON.
BRENDA	5.99.1.3. 74679.
Family and domain databases
HAMAP	MF_01125. [Tree]
InterPro	IPR003593. ATPase_AAA+_core. IPR014001. DEAD-like_N. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR003586. Hedgehog_hint_C. IPR003587. Hedgehog_hint_N. IPR014021. Helicase_SF1/SF2_ATP-bd. IPR004042. Intein_endonuc. IPR006141. Intein_splicing_site. IPR005736. Reverse_gyrase. 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. IPR006154. Toprim_dom_subgr. IPR006171. Toprim_domain. [Graphical view]
Gene3D	G3DSA:1.10.460.10. Topo_IA_cen_sub1. 1 hit. G3DSA:1.10.290.10. Topo_IA_cen_sub3. 1 hit.
PANTHER	PTHR11390. Topo_IA. 1 hit.
Pfam	PF00270. DEAD. 1 hit. PF01131. Topoisom_bac. 3 hits. PF01751. Toprim. 1 hit. [Graphical view]
PRINTS	PR00417. PRTPISMRASEI.
SMART	SM00382. AAA. 1 hit. SM00487. DEXDc. 1 hit. SM00305. HintC. 1 hit. SM00306. HintN. 1 hit. SM00437. TOP1Ac. 1 hit. SM00436. TOP1Bc. 1 hit. SM00493. TOPRIM. 1 hit. [Graphical view]
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS50818. INTEIN_C_TER. 1 hit. PS50819. INTEIN_ENDONUCLEASE. 1 hit. PS50817. INTEIN_N_TER. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RGYR_PYRHO

Accession

Primary (citable) accession number: O58530

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 16, 2004
Last sequence update:	August 1, 1998
Last modified:	December 15, 2009
This is version 64 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)