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O29238 (RGYR_ARCFU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Reverse gyrase

Including the following 2 domains:

  1. Helicase
    EC=3.6.4.12
  2. Topoisomerase
    EC=5.99.1.3
Gene names
Name:rgy
Ordered Locus Names:AF_1024
OrganismArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) [Reference proteome] [HAMAP]
Taxonomic identifier224325 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Archaeoglobi › Archaeoglobales › Archaeoglobaceae › Archaeoglobus ›

Protein attributes

Sequence length1054 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.3

Catalytic activity

ATP + H2O = ADP + phosphate. HAMAP-Rule MF_01125

ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP-Rule MF_01125

Cofactor

Magnesium. Binds two Mg2+ per subunit By similarity. HAMAP-Rule MF_01125

Subunit structure

Monomer.

Domain

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. Ref.2 Ref.3

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. HAMAP-Rule MF_01125

Sequence similarities

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 helicase ATP-binding domain.

Contains 1 Toprim domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10541054Reverse gyrase HAMAP-Rule MF_01125
PRO_0000158086

Regions

Domain65 – 245181Helicase ATP-binding
Domain506 – 662157Toprim
Zinc finger10 – 2718C4-type 1 HAMAP-Rule MF_01125
Nucleotide binding78 – 858ATP HAMAP-Rule MF_01125
Zinc finger584 – 60118C4-type 2 HAMAP-Rule MF_01125
Region512 – 1054543Topoisomerase I HAMAP-Rule MF_01125
Motif182 – 1854DEAD box HAMAP-Rule MF_01125

Sites

Active site8091For DNA cleavage activity
Metal binding5121Magnesium 1; catalytic By similarity
Metal binding6311Magnesium 1; catalytic By similarity
Metal binding6311Magnesium 2 By similarity
Metal binding6331Magnesium 2 By similarity
Binding site611ATP
Binding site841ATP
Binding site851ATP
Binding site861ATP

Experimental info

Mutagenesis8091Y → F: Loss of topoisomerase activity. Ref.2

Secondary structure

1 ................................................................................................................................................................................... 1054
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O29238 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: 551F19ADD62D7175

FASTA1,054121,315
        10         20         30         40         50         60 
MIPVVYSNLC PVCGGDLESK EIEKHVCFRK KRSLCLFPED FLLKEFVEFF RKCVGEPRAI 

        70         80         90        100        110        120 
QKMWAKRILR KESFAATAPT GVGKTSFGLA MSLFLALKGK RCYVIFPTSL LVIQAAETIR 

       130        140        150        160        170        180 
KYAEKAGVGT ENLIGYYHGR IPKREKENFM QNLRNFKIVI TTTQFLSKHY RELGHFDFIF 

       190        200        210        220        230        240 
VDDVDAILKA SKNVDKLLHL LGFHYDLKTK SWVGEARGCL MVSTATAKKG KKAELFRQLL 

       250        260        270        280        290        300 
NFDIGSSRIT VRNVEDVAVN DESISTLSSI LEKLGTGGII YARTGEEAEE IYESLKNKFR 

       310        320        330        340        350        360 
IGIVTATKKG DYEKFVEGEI DHLIGTAHYY GTLVRGLDLP ERIRFAVFVG CPSFRVTIED 

       370        380        390        400        410        420 
IDSLSPQMVK LLAYLYRNVD EIERLLPAVE RHIDEVREIL KKVMGKERPQ AKDVVVREGE 

       430        440        450        460        470        480 
VIFPDLRTYI QGSGRTSRLF AGGLTKGASF LLEDDSELLS AFIERAKLYD IEFKSIDEVD 

       490        500        510        520        530        540 
FEKLSRELDE SRDRYRRRQE FDLIKPALFI VESPTKARQI SRFFGKPSVK VLDGAVVYEI 

       550        560        570        580        590        600 
PMQKYVLMVT ASIGHVVDLI TNRGFHGVLV NGRFVPVYAS IKRCRDCGYQ FTEDRESCPK 

       610        620        630        640        650        660 
CGSENVDNSR SRIEALRKLA HDAEFVIVGT DPDTEGEKIA WDLKNLLSGC GAVKRAEFHE 

       670        680        690        700        710        720 
VTRRAILEAL ESLRDVDENL VKAQVVRRIE DRWIGFVLSQ KLWERFNNRN LSAGRAQTPV 

       730        740        750        760        770        780 
LGWIIDRFQE SRERRKIAIV RDFDLVLEHD EEEFDLTIKL VEEREELRTP LPPYTTETML 

       790        800        810        820        830        840 
SDANRILKFS VKQTMQIAQE LFENGLITYH RTDSTRVSDV GQRIAKEYLG DDFVGREWGE 

       850        860        870        880        890        900 
SGAHECIRPT RPLTRDDVQR LIQEGVLVVE GLRWEHFALY DLIFRRFMAS QCRPFKVVVK 

       910        920        930        940        950        960 
KYSIEFDGKT AEEERIVRAE GRAYELYRAV WVKNELPTGT FRVKAEVKSV PKVLPFTQSE 

       970        980        990       1000       1010       1020 
IIQMMKERGI GRPSTYATIV DRLFMRNYVV EKYGRMIPTK LGIDVFRFLV RRYAKFVSED 

      1030       1040       1050 
RTRDLESRMD AIERGELDYL KALEDLYAEI KSID

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE000782 Genomic DNA. Translation: AAB90219.1.
PIRH69377.
RefSeqNP_069857.1. NC_000917.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1GKUX-ray2.70B33-1054[»]
1GL9X-ray3.20B/C1-1054[»]
ProteinModelPortalO29238.
ModBaseSearch...

Protein-protein interaction databases

STRING224325.AF1024.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAB90219; AAB90219; AF_1024.
GeneID1484247.
KEGGafu:AF1024.

Phylogenomic databases

eggNOGCOG1110.
KOK03170.
OMAGEKISWD.
ProtClustDBPRK09401.

Enzyme and pathway databases

BioCycAFUL224325:GJBC-1046-MONOMER.

Family and domain databases

Gene3D1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPMF_01125. Reverse_gyrase.
InterProIPR011545. 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]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF00270. DEAD. 1 hit.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00417. PRTPISMRASEI.
SMARTSM00487. DEXDc. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 2 hits.
SSF56712. Topo_IA_core. 1 hit.
TIGRFAMsTIGR01054. rgy. 1 hit.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO29238.

Entry information

Entry nameRGYR_ARCFU
AccessionPrimary (citable) accession number: O29238
Entry history
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: January 1, 1998
Last modified: May 29, 2013
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents