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Q6F598 (RGYR_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 77. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Reverse gyrase

Cleaved into the following chain:

  1. Pko r-Gyr intein

Including the following 2 domains:

  1. Helicase
    EC=3.6.4.12
  2. Topoisomerase
    EC=5.99.1.3
Gene names
Name:rgy
Ordered Locus Names:TK0470
OrganismPyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]
Taxonomic identifier69014 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›

Protein attributes

Sequence length1711 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred 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. HAMAP-Rule MF_01125

Catalytic activity

ATP + H2O = ADP + phosphate. HAMAP-Rule MF_01125

ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP-Rule MF_01125

Cofactor

Magnesium. Binds two Mg2+ per subunit By similarity.

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. HAMAP-Rule MF_01125

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 By similarity. HAMAP-Rule MF_01125

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-Rule 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.

Contains 1 Toprim domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 960960Reverse gyrase, 1st part Potential
PRO_0000030359
Chain961 – 1449489Pko r-Gyr intein Potential
PRO_0000030360
Chain1450 – 1711262Reverse gyrase, 2nd part Potential
PRO_0000041880

Regions

Domain93 – 256164Helicase ATP-binding
Domain642 – 805164Toprim
Domain1160 – 1287128DOD-type homing endonuclease
Zinc finger9 – 3022C4-type 1 By similarity
Nucleotide binding106 – 1138ATP By similarity
Zinc finger725 – 74420C4-type 2 By similarity
Region648 – 17111064Topoisomerase I HAMAP-Rule MF_01125
Motif213 – 2164DEAD box HAMAP-Rule MF_01125

Sites

Active site14521For DNA cleavage activity By similarity
Metal binding6481Magnesium 1; catalytic By similarity
Metal binding7741Magnesium 1; catalytic By similarity
Metal binding7741Magnesium 2 By similarity
Metal binding7761Magnesium 2 By similarity
Binding site891ATP By similarity

Sequences

Sequence LengthMass (Da)Tools
Q6F598 [UniParc].

Last modified August 16, 2004. Version 1.
Checksum: 73F19BBF5409E127

FASTA1,711197,560
        10         20         30         40         50         60 
MKAVYREMCP NCWGRISDER LVMRNPCEEC LDEPVHADSY FQLVSAVRNA LKLRGTLKEW 

        70         80         90        100        110        120 
EKIYQLENQT REIEEFFKKA TGFTFWSAQR TWVKRLLKGR SFSIIAPTGM GKSTFGAFMA 

       130        140        150        160        170        180 
VWHALKGKKS YIVVPTTPLV IQTVRKIEGI MENANADVRL AYYHGNLRKK EKEEMLERIK 

       190        200        210        220        230        240 
NEDYDILVTS AQWLARNYEE VLKGRHFDFI FVDDVDAFLK ASKNIDRSLY LLGFTDEIIQ 

       250        260        270        280        290        300 
KAWEIIRLKK QMSRYLNGNS EDRNEKLNGL NREIEKLQRE IEKFKRKNKI GIMIIASATG 

       310        320        330        340        350        360 
SARGDRIKLY RELLGFEVGS GRSALRNVVD SYLKPTKDIK EHVEELLTRL GKGGLIFVPV 

       370        380        390        400        410        420 
DQGLGYAEEL ANYLSEKGFK IELVSSKNKK ALEKFENGEA DYLIGSATYY GSLVRGIDLP 

       430        440        450        460        470        480 
HLIRYAVFTG VPKFRFSIDL ERPTIYRALG LLSEIMDFLS EEDRRQAEKL HARLRRLIRN 

       490        500        510        520        530        540 
IPQFELLKIE EALAEGLPIE NEFHNHVLGV FRELVEFLRR VLRDEEVLRK LAEDPFISLV 

       550        560        570        580        590        600 
KEEGKWYIEI PDVRTYIQAT GRTSRLFAGG ITKGLSVLIV DNEKVFNGLV RQMRWRFQEF 

       610        620        630        640        650        660 
KMVPFEELDL DEILRQIDED REKVRLVMEG KISAKVKDLV RSALMIVESP NKARTIANFF 

       670        680        690        700        710        720 
GQPSKTRIGD LVAYEISVGD RMLTILASGG HMFDLVTNEG YHGVLIQNEG DMLKFIPVYD 

       730        740        750        760        770        780 
TLKRCRDCGH QFVDWEKKGV CPRCGSTNVR DALENVIAMR EIAQEVDEIL IATDPDTEGE 

       790        800        810        820        830        840 
KIAWDIRNVL APYTPNIKRI EFHEVTRPAI MKAIQEARDV NENRVNAQIV RRIEDRWIGF 

       850        860        870        880        890        900 
ELSQELQRVF ESYNLSAGRV QTPVLGWIIE RYKEFTESEV YFLGLTLENG LQVTIELGKD 

       910        920        930        940        950        960 
GKDVEPPEYV TVEEVQLEER ELNPAPPYTT DAMLKDASTF LKLSAPETMR LAQDLFEAGL 

       970        980        990       1000       1010       1020 
CVTPDTLVSL ADGRIMEIKD AVEKSEGNLL SVNGLKPKEA KALKFWEIDW NGPLKVIKLK 

      1030       1040       1050       1060       1070       1080 
NGHEIKATPD HGLLVMREGK LGWVSAKNVR EGDYVAFAYN TGHRGRDEYT LLKLMIKLGI 

      1090       1100       1110       1120       1130       1140 
TDVMVELDEE YFNEKVAPIV RERISTSTKY KYLRRRVLPL YLLQEWGLDD YEAHVKSLYR 

      1150       1160       1170       1180       1190       1200 
QRAGSKPIPN FKLDGRFWYV FGLVLGDGTL RDSKVLISQT PLKDVKSVLE DVFPFLRVFE 

      1210       1220       1230       1240       1250       1260 
TTNQVGFSNS IIAEVFRRLG ARKGKLHPLV FGLREEYINA MIAGYFDTDG TFSILNDRKG 

      1270       1280       1290       1300       1310       1320 
PNFRGILTSK RGDVLRMLSV YLYQIGIMNY LRRDERTGVW DLIISNRSLE KFREKIYPYL 

      1330       1340       1350       1360       1370       1380 
RIRRAQFDEA YSVYRASRRA FEGDLLPVAP VFGKLKFKNG TKNRILKETG IDVWNWLKRP 

      1390       1400       1410       1420       1430       1440 
EGEIPRDKLS KVLEYAEESP EKEFLKSLVE AGVTWVKVKG VEEELYTGKL YDFTTTTENF 

      1450       1460       1470       1480       1490       1500 
LSNGAVSHNC TYHRTDSTHV SNTGIEVAKE YITQELGEKY FKPRPWGEEG AHEAIRPTRP 

      1510       1520       1530       1540       1550       1560 
IDTGRLMQLI RDGIIQLPRN LTRNHYRLYD MIFRRFMTSQ MTPAKILYEK AVINAGVGKA 

      1570       1580       1590       1600       1610       1620 
ELEGYVEIIE DGWTRLRSPP LRELPKLEKG MKLKVVEAKK WKAPKVSLYT QGDIIALMKE 

      1630       1640       1650       1660       1670       1680 
RKIGRPSTYA KIVETLMRRG YVVETKGRKK LLPTEKGIKV YHYLVSKYRD LVSEERTREL 

      1690       1700       1710 
EEIMDRIEEG IEDYIKVLGE LYSEIQRYVS G

« Hide

References

« Hide 'large scale' references
[1]"Reverse gyrase is not a prerequisite for hyperthermophilic life."
Atomi H., Matsumi R., Imanaka T.
J. Bacteriol. 186:4829-4833(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes."
Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.
Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB117612 Genomic DNA. Translation: BAD26706.1.
AP006878 Genomic DNA. Translation: BAD84659.1.
RefSeqYP_182883.1. NC_006624.1.

3D structure databases

ProteinModelPortalQ6F598.
ModBaseSearch...

Protein-protein interaction databases

STRING69014.TK0470.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD84659; BAD84659; TK0470.
GeneID3234065.
KEGGtko:TK0470.

Phylogenomic databases

eggNOGCOG1110.
HOGENOMHOG000222775.
KOK03170.
OMAGWVSAKN.
ProtClustDBPRK14701.

Family and domain databases

Gene3D1.10.290.10. 2 hits.
1.10.460.10. 2 hits.
HAMAPMF_01125. Reverse_gyrase.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR005736. Reverse_gyrase.
IPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF00270. DEAD. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00417. PRTPISMRASEI.
SMARTSM00487. 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]
SUPFAMSSF56712. Topo_IA_core. 2 hits.
TIGRFAMsTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01054. rgy. 1 hit.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRGYR_PYRKO
AccessionPrimary (citable) accession number: Q6F598
Entry history
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: August 16, 2004
Last modified: May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Intein-containing proteins

List of intein-containing protein entries

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents