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O29238

- RGYR_ARCFU

UniProt

O29238 - RGYR_ARCFU

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Protein

Reverse gyrase

Gene
rgy, AF_1024
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.2 Publications

Catalytic activityi

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

Cofactori

Magnesium. Binds two Mg2+ per subunit By similarity.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; catalytic By similarity
Metal bindingi631 – 6311Magnesium 1; catalytic By similarity
Metal bindingi631 – 6311Magnesium 2 By similarity
Metal bindingi633 – 6331Magnesium 2 By similarity
Active sitei809 – 8091For DNA cleavage activity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 2718C4-type 1UniRule annotationAdd
BLAST
Nucleotide bindingi78 – 858ATPUniRule annotation
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 gyrase
Including the following 2 domains:
Helicase (EC:3.6.4.12)
Topoisomerase (EC:5.99.1.3)
Gene namesi
Name:rgy
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

Subcellular locationi

GO - Cellular componenti

  1. chromosome Source: InterPro
Complete GO annotation...

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 gyraseUniRule annotationPRO_0000158086Add
BLAST

Interactioni

Subunit structurei

Monomer.

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GKUX-ray2.70B33-1054[»]
1GL9X-ray3.20B/C1-1054[»]
ProteinModelPortaliO29238.

Miscellaneous databases

EvolutionaryTraceiO29238.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini65 – 245181Helicase ATP-bindingAdd
BLAST
Domaini506 – 662157ToprimAdd
BLAST

Region

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

Motif

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

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.2 Publications

Sequence similaritiesi

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 Toprim domain.

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. DNA/RNA_helicase_DEAD/DEAH_N.
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.
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

MIPVVYSNLC PVCGGDLESK EIEKHVCFRK KRSLCLFPED FLLKEFVEFF     50
RKCVGEPRAI QKMWAKRILR KESFAATAPT GVGKTSFGLA MSLFLALKGK 100
RCYVIFPTSL LVIQAAETIR KYAEKAGVGT ENLIGYYHGR IPKREKENFM 150
QNLRNFKIVI TTTQFLSKHY RELGHFDFIF VDDVDAILKA SKNVDKLLHL 200
LGFHYDLKTK SWVGEARGCL MVSTATAKKG KKAELFRQLL NFDIGSSRIT 250
VRNVEDVAVN DESISTLSSI LEKLGTGGII YARTGEEAEE IYESLKNKFR 300
IGIVTATKKG DYEKFVEGEI DHLIGTAHYY GTLVRGLDLP ERIRFAVFVG 350
CPSFRVTIED IDSLSPQMVK LLAYLYRNVD EIERLLPAVE RHIDEVREIL 400
KKVMGKERPQ AKDVVVREGE VIFPDLRTYI QGSGRTSRLF AGGLTKGASF 450
LLEDDSELLS AFIERAKLYD IEFKSIDEVD FEKLSRELDE SRDRYRRRQE 500
FDLIKPALFI VESPTKARQI SRFFGKPSVK VLDGAVVYEI PMQKYVLMVT 550
ASIGHVVDLI TNRGFHGVLV NGRFVPVYAS IKRCRDCGYQ FTEDRESCPK 600
CGSENVDNSR SRIEALRKLA HDAEFVIVGT DPDTEGEKIA WDLKNLLSGC 650
GAVKRAEFHE VTRRAILEAL ESLRDVDENL VKAQVVRRIE DRWIGFVLSQ 700
KLWERFNNRN LSAGRAQTPV LGWIIDRFQE SRERRKIAIV RDFDLVLEHD 750
EEEFDLTIKL VEEREELRTP LPPYTTETML SDANRILKFS VKQTMQIAQE 800
LFENGLITYH RTDSTRVSDV GQRIAKEYLG DDFVGREWGE SGAHECIRPT 850
RPLTRDDVQR LIQEGVLVVE GLRWEHFALY DLIFRRFMAS QCRPFKVVVK 900
KYSIEFDGKT AEEERIVRAE GRAYELYRAV WVKNELPTGT FRVKAEVKSV 950
PKVLPFTQSE IIQMMKERGI GRPSTYATIV DRLFMRNYVV EKYGRMIPTK 1000
LGIDVFRFLV RRYAKFVSED RTRDLESRMD AIERGELDYL KALEDLYAEI 1050
KSID 1054
Length:1,054
Mass (Da):121,315
Last modified:January 1, 1998 - v1
Checksum:i551F19ADD62D7175
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE000782 Genomic DNA. Translation: AAB90219.1.
PIRiH69377.
RefSeqiNP_069857.1. NC_000917.1.
WP_010878524.1. NC_000917.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE000782 Genomic DNA. Translation: AAB90219.1 .
PIRi H69377.
RefSeqi NP_069857.1. NC_000917.1.
WP_010878524.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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. DNA/RNA_helicase_DEAD/DEAH_N.
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.
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: September 3, 2014
This is version 110 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

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