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Protein

Reverse gyrase

Gene

rgy

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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.

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei61ATP1
Binding sitei84ATP1
Binding sitei85ATP1
Binding sitei86ATP1
Metal bindingi512Magnesium 1; catalyticUniRule annotation1
Metal bindingi631Magnesium 1; catalyticUniRule annotation1
Metal bindingi631Magnesium 2UniRule annotation1
Metal bindingi633Magnesium 2UniRule annotation1
Active sitei809For DNA cleavage activity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri10 – 27C4-type 1UniRule annotationAdd BLAST18
Nucleotide bindingi78 – 85ATP8
Zinc fingeri584 – 601C4-type 2UniRule annotationAdd BLAST18

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

Enzyme and pathway databases

BRENDAi5.99.1.3. 414.

Names & Taxonomyi

Protein namesi
Recommended name:
Reverse gyraseUniRule annotation
Including the following 2 domains:
HelicaseUniRule annotation (EC:3.6.4.12UniRule annotation)
TopoisomeraseUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:rgyUniRule annotation
Ordered Locus Names:AF_1024
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi809Y → F: Loss of topoisomerase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001580861 – 1054Reverse gyraseAdd BLAST1054

Interactioni

Subunit structurei

Monomer.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi224325.AF1024.

Structurei

Secondary structure

11054
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi19 – 21Combined sources3
Helixi40 – 51Combined sources12
Turni52 – 54Combined sources3
Helixi59 – 69Combined sources11
Beta strandi74 – 76Combined sources3
Helixi85 – 96Combined sources12
Turni97 – 99Combined sources3
Beta strandi102 – 107Combined sources6
Helixi109 – 123Combined sources15
Turni124 – 126Combined sources3
Helixi130 – 132Combined sources3
Beta strandi133 – 136Combined sources4
Helixi144 – 151Combined sources8
Helixi153 – 155Combined sources3
Beta strandi157 – 162Combined sources6
Helixi163 – 168Combined sources6
Beta strandi170 – 173Combined sources4
Beta strandi177 – 182Combined sources6
Helixi184 – 188Combined sources5
Helixi192 – 200Combined sources9
Beta strandi203 – 206Combined sources4
Turni207 – 210Combined sources4
Beta strandi211 – 214Combined sources4
Beta strandi217 – 222Combined sources6
Beta strandi225 – 227Combined sources3
Helixi233 – 240Combined sources8
Beta strandi254 – 260Combined sources7
Turni264 – 267Combined sources4
Helixi268 – 271Combined sources4
Beta strandi278 – 284Combined sources7
Helixi285 – 293Combined sources9
Turni294 – 297Combined sources4
Beta strandi301 – 303Combined sources3
Beta strandi307 – 309Combined sources3
Helixi310 – 316Combined sources7
Beta strandi321 – 326Combined sources6
Helixi327 – 332Combined sources6
Helixi334 – 336Combined sources3
Turni340 – 342Combined sources3
Beta strandi345 – 350Combined sources6
Beta strandi353 – 357Combined sources5
Turni358 – 360Combined sources3
Helixi361 – 363Combined sources3
Helixi366 – 373Combined sources8
Turni374 – 376Combined sources3
Helixi379 – 383Combined sources5
Turni387 – 389Combined sources3
Helixi393 – 404Combined sources12
Beta strandi412 – 417Combined sources6
Beta strandi420 – 424Combined sources5
Helixi426 – 434Combined sources9
Beta strandi447 – 452Combined sources6
Helixi456 – 467Combined sources12
Helixi481 – 496Combined sources16
Helixi498 – 500Combined sources3
Beta strandi505 – 512Combined sources8
Helixi514 – 521Combined sources8
Helixi522 – 524Combined sources3
Beta strandi528 – 532Combined sources5
Beta strandi535 – 541Combined sources7
Beta strandi543 – 551Combined sources9
Beta strandi556 – 559Combined sources4
Beta strandi561 – 564Combined sources4
Beta strandi571 – 573Combined sources3
Beta strandi577 – 580Combined sources4
Helixi609 – 623Combined sources15
Beta strandi624 – 628Combined sources5
Helixi634 – 647Combined sources14
Beta strandi650 – 655Combined sources6
Helixi663 – 670Combined sources8
Helixi678 – 704Combined sources27
Turni705 – 707Combined sources3
Helixi717 – 728Combined sources12
Helixi730 – 732Combined sources3
Beta strandi733 – 740Combined sources8
Turni741 – 744Combined sources4
Beta strandi745 – 748Combined sources4
Beta strandi752 – 768Combined sources17
Helixi776 – 785Combined sources10
Helixi791 – 803Combined sources13
Beta strandi806 – 808Combined sources3
Helixi819 – 829Combined sources11
Beta strandi830 – 833Combined sources4
Beta strandi849 – 852Combined sources4
Helixi855 – 864Combined sources10
Helixi874 – 889Combined sources16
Beta strandi895 – 906Combined sources12
Beta strandi909 – 913Combined sources5
Beta strandi916 – 921Combined sources6
Helixi922 – 926Combined sources5
Beta strandi939 – 945Combined sources7
Beta strandi948 – 953Combined sources6
Helixi958 – 968Combined sources11
Turni973 – 975Combined sources3
Helixi976 – 985Combined sources10
Beta strandi988 – 992Combined sources5
Beta strandi995 – 998Combined sources4
Helixi1000 – 1011Combined sources12
Helixi1015 – 1017Combined sources3
Helixi1019 – 1034Combined sources16
Helixi1039 – 1051Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GKUX-ray2.70B33-1054[»]
1GL9X-ray3.20B/C1-1054[»]
ProteinModelPortaliO29238.
SMRiO29238.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29238.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini65 – 245Helicase ATP-bindingUniRule annotationAdd BLAST181
Domaini506 – 662ToprimUniRule annotationAdd BLAST157

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni512 – 1054Topoisomerase IAdd BLAST543

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi182 – 185DEAD 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.

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri10 – 27C4-type 1UniRule annotationAdd BLAST18
Zinc fingeri584 – 601C4-type 2UniRule annotationAdd BLAST18

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiarCOG01526. Archaea.
COG1110. LUCA.
KOiK03170.
OMAiRIEMHEI.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
3.40.50.300. 3 hits.
HAMAPiMF_01125. Reverse_gyrase. 1 hit.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
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. 1 hit.
PfamiPF00270. DEAD. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00487. DEXDc. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01054. rgy. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O29238-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIPVVYSNLC PVCGGDLESK EIEKHVCFRK KRSLCLFPED FLLKEFVEFF
60 70 80 90 100
RKCVGEPRAI QKMWAKRILR KESFAATAPT GVGKTSFGLA MSLFLALKGK
110 120 130 140 150
RCYVIFPTSL LVIQAAETIR KYAEKAGVGT ENLIGYYHGR IPKREKENFM
160 170 180 190 200
QNLRNFKIVI TTTQFLSKHY RELGHFDFIF VDDVDAILKA SKNVDKLLHL
210 220 230 240 250
LGFHYDLKTK SWVGEARGCL MVSTATAKKG KKAELFRQLL NFDIGSSRIT
260 270 280 290 300
VRNVEDVAVN DESISTLSSI LEKLGTGGII YARTGEEAEE IYESLKNKFR
310 320 330 340 350
IGIVTATKKG DYEKFVEGEI DHLIGTAHYY GTLVRGLDLP ERIRFAVFVG
360 370 380 390 400
CPSFRVTIED IDSLSPQMVK LLAYLYRNVD EIERLLPAVE RHIDEVREIL
410 420 430 440 450
KKVMGKERPQ AKDVVVREGE VIFPDLRTYI QGSGRTSRLF AGGLTKGASF
460 470 480 490 500
LLEDDSELLS AFIERAKLYD IEFKSIDEVD FEKLSRELDE SRDRYRRRQE
510 520 530 540 550
FDLIKPALFI VESPTKARQI SRFFGKPSVK VLDGAVVYEI PMQKYVLMVT
560 570 580 590 600
ASIGHVVDLI TNRGFHGVLV NGRFVPVYAS IKRCRDCGYQ FTEDRESCPK
610 620 630 640 650
CGSENVDNSR SRIEALRKLA HDAEFVIVGT DPDTEGEKIA WDLKNLLSGC
660 670 680 690 700
GAVKRAEFHE VTRRAILEAL ESLRDVDENL VKAQVVRRIE DRWIGFVLSQ
710 720 730 740 750
KLWERFNNRN LSAGRAQTPV LGWIIDRFQE SRERRKIAIV RDFDLVLEHD
760 770 780 790 800
EEEFDLTIKL VEEREELRTP LPPYTTETML SDANRILKFS VKQTMQIAQE
810 820 830 840 850
LFENGLITYH RTDSTRVSDV GQRIAKEYLG DDFVGREWGE SGAHECIRPT
860 870 880 890 900
RPLTRDDVQR LIQEGVLVVE GLRWEHFALY DLIFRRFMAS QCRPFKVVVK
910 920 930 940 950
KYSIEFDGKT AEEERIVRAE GRAYELYRAV WVKNELPTGT FRVKAEVKSV
960 970 980 990 1000
PKVLPFTQSE IIQMMKERGI GRPSTYATIV DRLFMRNYVV EKYGRMIPTK
1010 1020 1030 1040 1050
LGIDVFRFLV RRYAKFVSED RTRDLESRMD AIERGELDYL KALEDLYAEI

KSID
Length:1,054
Mass (Da):121,315
Last modified:January 1, 1998 - v1
Checksum:i551F19ADD62D7175
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90219.1.
PIRiH69377.
RefSeqiWP_010878524.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90219; AAB90219; AF_1024.
GeneIDi1484247.
KEGGiafu:AF_1024.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90219.1.
PIRiH69377.
RefSeqiWP_010878524.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GKUX-ray2.70B33-1054[»]
1GL9X-ray3.20B/C1-1054[»]
ProteinModelPortaliO29238.
SMRiO29238.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF1024.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90219; AAB90219; AF_1024.
GeneIDi1484247.
KEGGiafu:AF_1024.

Phylogenomic databases

eggNOGiarCOG01526. Archaea.
COG1110. LUCA.
KOiK03170.
OMAiRIEMHEI.

Enzyme and pathway databases

BRENDAi5.99.1.3. 414.

Miscellaneous databases

EvolutionaryTraceiO29238.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
3.40.50.300. 3 hits.
HAMAPiMF_01125. Reverse_gyrase. 1 hit.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
IPR014001. Helicase_ATP-bd.
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. 1 hit.
PfamiPF00270. DEAD. 1 hit.
PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00487. DEXDc. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
SSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01054. rgy. 1 hit.
PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRGYR_ARCFU
AccessioniPrimary (citable) accession number: O29238
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: January 1, 1998
Last modified: November 2, 2016
This is version 122 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.