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Protein

Reverse gyrase

Gene

rgy

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

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).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.
ATP-dependent breakage, passage and rejoining of double-stranded DNA.

Cofactori

Mg2+By similarityNote: Binds two Mg2+ per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei83 – 831ATPBy similarity
Metal bindingi556 – 5561Magnesium 1; catalyticBy similarity
Metal bindingi681 – 6811Magnesium 1; catalyticBy similarity
Metal bindingi681 – 6811Magnesium 2By similarity
Metal bindingi683 – 6831Magnesium 2By similarity
Active sitei1363 – 13631For DNA cleavage activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 3021C4-typeBy similarityAdd
BLAST
Nucleotide bindingi100 – 1078ATPBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase, Isomerase, Topoisomerase

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Reverse gyrase
Cleaved into the following chain:
Including the following 2 domains:
Helicase (EC:3.6.4.12)
Topoisomerase (EC:5.99.1.3)
Gene namesi
Name:rgy
Ordered Locus Names:MJ1512
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 866866Reverse gyrase, 1st partSequence analysisPRO_0000030353Add
BLAST
Chaini867 – 1360494Mja r-Gyr inteinSequence analysisPRO_0000030354Add
BLAST
Chaini1361 – 1613253Reverse gyrase, 2nd partSequence analysisPRO_0000030355Add
BLAST

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Proteomic databases

PRIDEiQ58907.

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi243232.MJ_1512.

Structurei

3D structure databases

ProteinModelPortaliQ58907.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini87 – 291205Helicase ATP-bindingAdd
BLAST
Domaini310 – 525216Helicase C-terminalAdd
BLAST
Domaini550 – 712163ToprimAdd
BLAST
Domaini1070 – 1199130DOD-type homing endonucleaseAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni556 – 16131058Topoisomerase IAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi203 – 2064DEAD box

Domaini

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).By similarity

Sequence similaritiesi

In the N-terminal section; belongs to the DEAD box helicase family. DDVD subfamily.Curated
In the C-terminal section; belongs to the prokaryotic type I/III topoisomerase family.Curated
Contains 1 helicase ATP-binding domain.Curated
Contains 1 helicase C-terminal domain.Curated
Contains 1 Toprim domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 3021C4-typeBy similarityAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiarCOG01526. Archaea.
arCOG03145. Archaea.
COG1110. LUCA.
InParanoidiQ58907.
KOiK03170.
OMAiGWVSAKN.
PhylomeDBiQ58907.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 2 hits.
1.10.460.10. 2 hits.
2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
3.40.50.140. 1 hit.
3.40.50.300. 3 hits.
HAMAPiMF_01125. Reverse_gyrase. 1 hit.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028992. Hedgehog/Intein_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR027417. P-loop_NTPase.
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_dom.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 3 hits.
PfamiPF00270. DEAD. 1 hit.
PF14528. LAGLIDADG_3. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
PR00417. PRTPISMRASEI.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 3 hits.
SSF52540. SSF52540. 2 hits.
SSF55608. SSF55608. 1 hit.
SSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01054. rgy. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 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]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q58907-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIPMIYKEMC PNCNGEITSE RLAIGVCEKC LKEENVFEKL KLCEKLREEK
60 70 80 90 100
TLKNLKDYCI IWNEFKEFEE FVKDLGFELL SIQKMWAKRV LKNKSFSIVV
110 120 130 140 150
PTGVGKSFFG ILMSLFLAKK GKRCYIILPT TLLVKQTYEK ISSLTEKNNL
160 170 180 190 200
NIRVVAYHSE LSTKEKKEVK ERIENNDYDV LITTSNYLTK NMPKCKFDFV
210 220 230 240 250
FVDDVDALLK ASKNIDRTLK LLGFDEEIIN EAYKIIYLIK IGKIEDAMKK
260 270 280 290 300
REILKKKISK IKHGCLIIAS ATGKSYGDRV KLYRELLDFE IGFGMNKLRD
310 320 330 340 350
VVDIYDEEFS KEKILEYIKL FGSGGIVFVS IDYGVEKAQE IEKYLLENNI
360 370 380 390 400
KAKLIHSKDK KGFDDFREGK IDVLIGVASY YGVLVRGLDM PERVRYAIFY
410 420 430 440 450
GIPKFKIRLK EYINSLKEKG ELKEDINIEG KTEEEIRQII TEKLKIKNFS
460 470 480 490 500
LRKEDDEYLL LIPDVKTYIQ ASGRTSRMTE FGLTKGASIV LVDEKEIFEA
510 520 530 540 550
LKKYMLFMYE SEFKRIDEVN LEELIKKIDE DREKIKVGRA KGKVPDLLKS
560 570 580 590 600
VLMVVESPNK ARTIANFFGK PSVRKINNRN VYEVCIGDLN LIITASGGHV
610 620 630 640 650
FDLVTKEGFY GVKIENNLYI PIYTSIKKVN GEQFTDQKDL EELIKQLMEK
660 670 680 690 700
GERVNAMDAK ENIEIIREIA DEVDAIFIAT DIDTEGEKIG YDIAINALPF
710 720 730 740 750
NRNIYRVGFN EITKRAILKA VESFKKGEEL SLDENKVKGQ VVRRIEDRWI
760 770 780 790 800
GFRLSQKLWE VFNKNYLSAG RVQTPVLGWI IERYNEHKIK VPYLSLKLEN
810 820 830 840 850
DIYIGKIWED EFDKDEVEVE VKVYEKEIPP LPPFTTDTLL EEATKRFGLS
860 870 880 890 900
TDEIMSIAQE LFELGLCLTP DTYVVLGDGR IETIEDIVNA KERNVLSLDL
910 920 930 940 950
DNLSIKIDTA IKFWKLRYNG NLSKITLSNN YELKATPDHC LLVLRDNQLK
960 970 980 990 1000
WIPAKDIKEN DYIAMPFNYK VERKPISLLN LLKYLDITDV LIEFDENSTI
1010 1020 1030 1040 1050
FEKIAEYIRN NIKTSTKYKY LRNRRVPLKY LIEWNFDLDE IEKEAKYIYK
1060 1070 1080 1090 1100
SVAGTKKIPL FKLDERFWYF AGLVLGDGSI QDSKIRIAQT PLKDVKSILD
1110 1120 1130 1140 1150
ETFPFLHNWI SGNQVIISNP IIAEILEKLG MRNGKLNGII FSLPESYINA
1160 1170 1180 1190 1200
LIAGYFDTDG CFSLLYDKKA KKHNLRMVLT SKRRDVLEKI GIYLNSIGIL
1210 1220 1230 1240 1250
NTLHKSREVY SLIISNKSLE TFKEKIAKYL KIRKEAFING YKTYKKEHEE
1260 1270 1280 1290 1300
RFECDLLPVK EVFKKLTFEK GRKEILKDSK IHIENWYKEK TNNIPREKLK
1310 1320 1330 1340 1350
TVLRYANNSE HKEFLEKIVN GDISFVRVKK VENIPYDGYV YDLSIKHNQN
1360 1370 1380 1390 1400
FISNGVISHN CTYHRTSSTR VSLDGMRVAR EYLKLNNLED YLKNREYFME
1410 1420 1430 1440 1450
GAHECIRPTK PMNTDELIEF LKENNIKLTK NHIKVYDLIF RRFIASQMKE
1460 1470 1480 1490 1500
AVVEYEEIYI KDLDEKVEGY VDIKFDGWSR IYNLKLKKLP RIEKSSLKVL
1510 1520 1530 1540 1550
DKKLRKIPKV PLYDEGEVVK LMKERGIGRP STYAQIIKKL LDRGYVVKSK
1560 1570 1580 1590 1600
DKNKLIPTKL GIEVYNYLIN NYPHLISEER TRELEEIMDK IENGEVDYIE
1610
VLKALHEEIL SIR
Length:1,613
Mass (Da):188,257
Last modified:November 1, 1996 - v1
Checksum:i7170C4E120237AE3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99531.1.
PIRiG64488.

Genome annotation databases

EnsemblBacteriaiAAB99531; AAB99531; MJ_1512.
KEGGimja:MJ_1512.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB99531.1.
PIRiG64488.

3D structure databases

ProteinModelPortaliQ58907.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_1512.

Proteomic databases

PRIDEiQ58907.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB99531; AAB99531; MJ_1512.
KEGGimja:MJ_1512.

Phylogenomic databases

eggNOGiarCOG01526. Archaea.
arCOG03145. Archaea.
COG1110. LUCA.
InParanoidiQ58907.
KOiK03170.
OMAiGWVSAKN.
PhylomeDBiQ58907.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 2 hits.
1.10.460.10. 2 hits.
2.170.16.10. 2 hits.
3.10.28.10. 1 hit.
3.40.50.140. 1 hit.
3.40.50.300. 3 hits.
HAMAPiMF_01125. Reverse_gyrase. 1 hit.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR028992. Hedgehog/Intein_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR004860. LAGLIDADG_2.
IPR027417. P-loop_NTPase.
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_dom.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 3 hits.
PfamiPF00270. DEAD. 1 hit.
PF14528. LAGLIDADG_3. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
PR00417. PRTPISMRASEI.
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 3 hits.
SSF52540. SSF52540. 2 hits.
SSF55608. SSF55608. 1 hit.
SSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01054. rgy. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 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]
ProtoNetiSearch...

Entry informationi

Entry nameiRGYR_METJA
AccessioniPrimary (citable) accession number: Q58907
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.