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O29238

- RGYR_ARCFU

UniProt

O29238 - RGYR_ARCFU

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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: 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 Mg(2+) per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei61 – 611ATP
Binding sitei84 – 841ATP
Binding sitei85 – 851ATP
Binding sitei86 – 861ATP
Metal bindingi512 – 5121Magnesium 1; catalyticUniRule annotation
Metal bindingi631 – 6311Magnesium 1; catalyticUniRule annotation
Metal bindingi631 – 6311Magnesium 2UniRule annotation
Metal bindingi633 – 6331Magnesium 2UniRule annotation
Active sitei809 – 8091For DNA cleavage activity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 2718C4-type 1UniRule annotationAdd
BLAST
Nucleotide bindingi78 – 858ATP
Zinc fingeri584 – 60118C4-type 2UniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type I activity Source: InterPro
  4. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-HAMAP
  5. helicase activity Source: UniProtKB-HAMAP
  6. magnesium ion binding Source: UniProtKB-HAMAP
  7. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA topological change Source: UniProtKB-HAMAP
  2. DNA unwinding involved in DNA replication Source: UniProtKB-HAMAP
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

BioCyciAFUL224325:GJBC-1046-MONOMER.

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
ProteomesiUP000002199: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi809 – 8091Y → F: Loss of topoisomerase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10541054Reverse gyrasePRO_0000158086Add
BLAST

Interactioni

Subunit structurei

Monomer.1 PublicationUniRule annotation

Protein-protein interaction databases

STRINGi224325.AF1024.

Structurei

Secondary structure

1
1054
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi19 – 213Combined sources
Helixi40 – 5112Combined sources
Turni52 – 543Combined sources
Helixi59 – 6911Combined sources
Beta strandi74 – 763Combined sources
Helixi85 – 9612Combined sources
Turni97 – 993Combined sources
Beta strandi102 – 1076Combined sources
Helixi109 – 12315Combined sources
Turni124 – 1263Combined sources
Helixi130 – 1323Combined sources
Beta strandi133 – 1364Combined sources
Helixi144 – 1518Combined sources
Helixi153 – 1553Combined sources
Beta strandi157 – 1626Combined sources
Helixi163 – 1686Combined sources
Beta strandi170 – 1734Combined sources
Beta strandi177 – 1826Combined sources
Helixi184 – 1885Combined sources
Helixi192 – 2009Combined sources
Beta strandi203 – 2064Combined sources
Turni207 – 2104Combined sources
Beta strandi211 – 2144Combined sources
Beta strandi217 – 2226Combined sources
Beta strandi225 – 2273Combined sources
Helixi233 – 2408Combined sources
Beta strandi254 – 2607Combined sources
Turni264 – 2674Combined sources
Helixi268 – 2714Combined sources
Beta strandi278 – 2847Combined sources
Helixi285 – 2939Combined sources
Turni294 – 2974Combined sources
Beta strandi301 – 3033Combined sources
Beta strandi307 – 3093Combined sources
Helixi310 – 3167Combined sources
Beta strandi321 – 3266Combined sources
Helixi327 – 3326Combined sources
Helixi334 – 3363Combined sources
Turni340 – 3423Combined sources
Beta strandi345 – 3506Combined sources
Beta strandi353 – 3575Combined sources
Turni358 – 3603Combined sources
Helixi361 – 3633Combined sources
Helixi366 – 3738Combined sources
Turni374 – 3763Combined sources
Helixi379 – 3835Combined sources
Turni387 – 3893Combined sources
Helixi393 – 40412Combined sources
Beta strandi412 – 4176Combined sources
Beta strandi420 – 4245Combined sources
Helixi426 – 4349Combined sources
Beta strandi447 – 4526Combined sources
Helixi456 – 46712Combined sources
Helixi481 – 49616Combined sources
Helixi498 – 5003Combined sources
Beta strandi505 – 5128Combined sources
Helixi514 – 5218Combined sources
Helixi522 – 5243Combined sources
Beta strandi528 – 5325Combined sources
Beta strandi535 – 5417Combined sources
Beta strandi543 – 5519Combined sources
Beta strandi556 – 5594Combined sources
Beta strandi561 – 5644Combined sources
Beta strandi571 – 5733Combined sources
Beta strandi577 – 5804Combined sources
Helixi609 – 62315Combined sources
Beta strandi624 – 6285Combined sources
Helixi634 – 64714Combined sources
Beta strandi650 – 6556Combined sources
Helixi663 – 6708Combined sources
Helixi678 – 70427Combined sources
Turni705 – 7073Combined sources
Helixi717 – 72812Combined sources
Helixi730 – 7323Combined sources
Beta strandi733 – 7408Combined sources
Turni741 – 7444Combined sources
Beta strandi745 – 7484Combined sources
Beta strandi752 – 76817Combined sources
Helixi776 – 78510Combined sources
Helixi791 – 80313Combined sources
Beta strandi806 – 8083Combined sources
Helixi819 – 82911Combined sources
Beta strandi830 – 8334Combined sources
Beta strandi849 – 8524Combined sources
Helixi855 – 86410Combined sources
Helixi874 – 88916Combined sources
Beta strandi895 – 90612Combined sources
Beta strandi909 – 9135Combined sources
Beta strandi916 – 9216Combined sources
Helixi922 – 9265Combined sources
Beta strandi939 – 9457Combined sources
Beta strandi948 – 9536Combined sources
Helixi958 – 96811Combined sources
Turni973 – 9753Combined sources
Helixi976 – 98510Combined sources
Beta strandi988 – 9925Combined sources
Beta strandi995 – 9984Combined sources
Helixi1000 – 101112Combined sources
Helixi1015 – 10173Combined sources
Helixi1019 – 103416Combined sources
Helixi1039 – 105113Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO29238.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini65 – 245181Helicase ATP-bindingUniRule annotationAdd
BLAST
Domaini506 – 662157ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni512 – 1054543Topoisomerase IAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi182 – 1854DEAD 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.

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 2718C4-type 1UniRule annotationAdd
BLAST
Zinc fingeri584 – 60118C4-type 2UniRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG1110.
KOiK03170.
OMAiTMRIAQD.

Family and domain databases

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.
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. 1 hit.
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.
RefSeqiNP_069857.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90219; AAB90219; AF_1024.
GeneIDi1484247.
KEGGiafu:AF1024.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90219.1 .
PIRi H69377.
RefSeqi NP_069857.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1GKU X-ray 2.70 B 33-1054 [» ]
1GL9 X-ray 3.20 B/C 1-1054 [» ]
ProteinModelPortali O29238.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 224325.AF1024.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAB90219 ; AAB90219 ; AF_1024 .
GeneIDi 1484247.
KEGGi afu:AF1024.

Phylogenomic databases

eggNOGi COG1110.
KOi K03170.
OMAi TMRIAQD.

Enzyme and pathway databases

BioCyci AFUL224325:GJBC-1046-MONOMER.

Miscellaneous databases

EvolutionaryTracei O29238.

Family and domain databases

Gene3Di 1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
3.40.50.300. 3 hits.
HAMAPi MF_01125. Reverse_gyrase.
InterProi IPR011545. 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 ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF00270. DEAD. 1 hit.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00417. PRTPISMRASEI.
SMARTi SM00487. DEXDc. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 2 hits.
SSF56712. SSF56712. 1 hit.
TIGRFAMsi TIGR01054. rgy. 1 hit.
PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. "Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional 'latch' in the mechanism of reverse gyrase."
    Rodriguez A.C.
    J. Biol. Chem. 277:29865-29873(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: N-TERMINAL DOMAIN FUNCTIONAL CHARACTERIZATION, MUTAGENESIS OF TYR-809.
  3. "Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase."
    Rodriguez A.C.
    Biochemistry 42:5993-6004(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: N-TERMINAL DOMAIN FUNCTIONAL CHARACTERIZATION.
  4. "Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA."
    Rodriguez A.C., Stock D.
    EMBO J. 21:418-426(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 38-1054 AND IN COMPLEX WITH ADENYLYLIMIDODIPHOSPHATE (ADPNP).
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.

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 26, 2014
This is version 113 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

External Data

Dasty 3