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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: -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

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.

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)DescriptionActionsGraphical viewLength
Binding sitei83ATPBy similarity1
Metal bindingi556Magnesium 1; catalyticBy similarity1
Metal bindingi681Magnesium 1; catalyticBy similarity1
Metal bindingi681Magnesium 2By similarity1
Metal bindingi683Magnesium 2By similarity1
Active sitei1363For DNA cleavage activityBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri10 – 30C4-typeBy similarityAdd BLAST21
Nucleotide bindingi100 – 107ATPBy similarity8

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Helicase, Hydrolase, Isomerase, Topoisomerase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciMJAN243232:G1GKE-1638-MONOMER

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000303531 – 866Reverse gyrase, 1st partSequence analysisAdd BLAST866
ChainiPRO_0000030354867 – 1360Mja r-Gyr inteinSequence analysisAdd BLAST494
ChainiPRO_00000303551361 – 1613Reverse gyrase, 2nd partSequence analysisAdd BLAST253

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
SMRiQ58907
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini87 – 291Helicase ATP-bindingAdd BLAST205
Domaini310 – 525Helicase C-terminalAdd BLAST216
Domaini550 – 712ToprimAdd BLAST163
Domaini1070 – 1199DOD-type homing endonucleaseAdd BLAST130

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni556 – 1613Topoisomerase IAdd BLAST1058

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi203 – 206DEAD box4

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri10 – 30C4-typeBy similarityAdd BLAST21

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiarCOG01526 Archaea
arCOG03145 Archaea
COG1110 LUCA
InParanoidiQ58907
KOiK03170
OMAiGVATYYG
OrthoDBiPOG093Z0046
PhylomeDBiQ58907

Family and domain databases

CDDicd00079 HELICc, 1 hit
cd00186 TOP1Ac, 1 hit
cd03361 TOPRIM_TopoIA_RevGyr, 1 hit
Gene3Di1.10.290.10, 2 hits
1.10.460.10, 2 hits
3.10.28.10, 1 hit
HAMAPiMF_01125 Reverse_gyrase, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR003586 Hint_dom_C
IPR003587 Hint_dom_N
IPR036844 Hint_dom_sf
IPR027434 Homing_endonucl
IPR006142 INTEIN
IPR030934 Intein_C
IPR004042 Intein_endonuc
IPR006141 Intein_N
IPR004860 LAGLIDADG_2
IPR027417 P-loop_NTPase
IPR005736 Reverse_gyrase
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
IPR034142 TOPRIM_RevGyr
PANTHERiPTHR43505 PTHR43505, 1 hit
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF14528 LAGLIDADG_3, 1 hit
PF01131 Topoisom_bac, 2 hits
PF01751 Toprim, 1 hit
PRINTSiPR00379 INTEIN
PR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00487 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
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
PROSITEiView protein in PROSITE
PS51192 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

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
RefSeqiWP_010871035.1, NC_000909.1

Genome annotation databases

EnsemblBacteriaiAAB99531; AAB99531; MJ_1512
GeneIDi1452419
KEGGimja:MJ_1512

Similar proteinsi

Entry informationi

Entry nameiRGYR_METJA
AccessioniPrimary (citable) accession number: Q58907
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: November 1, 1996
Last modified: February 28, 2018
This is version 130 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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