ID RGYR1_SULAC Reviewed; 1248 AA.
AC Q08582; Q4JAH3;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 27-MAR-2024, entry version 156.
DE RecName: Full=Reverse gyrase 1 {ECO:0000255|HAMAP-Rule:MF_01125, ECO:0000303|PubMed:6328327};
DE EC=5.6.2.- {ECO:0000255|HAMAP-Rule:MF_01125, ECO:0000269|PubMed:10748189, ECO:0000269|PubMed:14708549, ECO:0000269|PubMed:2853975, ECO:0000269|PubMed:3038879, ECO:0000269|PubMed:6328327};
GN Name=rgy1 {ECO:0000255|HAMAP-Rule:MF_01125};
GN Synonyms=top-rg {ECO:0000303|PubMed:8389456},
GN topR1 {ECO:0000303|PubMed:17307872}; OrderedLocusNames=Saci_0839;
OS Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC
OS 15157 / NCIMB 11770).
OC Archaea; Thermoproteota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Sulfolobus.
OX NCBI_TaxID=330779;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 141-149; 167-180;
RP 254-261; 427-432; 612-622; 881-887; 1036-1043; 1080-1086 AND 1239-1247, AND
RP DOMAIN.
RC STRAIN=ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770;
RX PubMed=8389456; DOI=10.1073/pnas.90.10.4753;
RA Confalonieri F., Elie C., Nadal M., de la Tour C.B., Forterre P.,
RA Duguet M.;
RT "Reverse gyrase: a helicase-like domain and a type I topoisomerase in the
RT same polypeptide.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:4753-4757(1993).
RN [2]
RP ERRATUM OF PUBMED:8389456.
RA Confalonieri F., Elie C., Nadal M., de la Tour C.B., Forterre P.,
RA Duguet M.;
RL Proc. Natl. Acad. Sci. U.S.A. 91:3478-3478(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770;
RX PubMed=15995215; DOI=10.1128/jb.187.14.4992-4999.2005;
RA Chen L., Bruegger K., Skovgaard M., Redder P., She Q., Torarinsson E.,
RA Greve B., Awayez M., Zibat A., Klenk H.-P., Garrett R.A.;
RT "The genome of Sulfolobus acidocaldarius, a model organism of the
RT Crenarchaeota.";
RL J. Bacteriol. 187:4992-4999(2005).
RN [4]
RP FUNCTION, AND COFACTOR.
RC STRAIN=FERM P-7137;
RX PubMed=6328327; DOI=10.1038/309677a0;
RA Kikuchi A., Asai K.;
RT "Reverse gyrase--a topoisomerase which introduces positive superhelical
RT turns into DNA.";
RL Nature 309:677-681(1984).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770;
RX PubMed=14708549; DOI=10.1002/j.1460-2075.1985.tb03902.x;
RA Forterre P., Mirambeau G., Jaxel C., Nadal M., Duguet M.;
RT "High positive supercoiling in vitro catalyzed by an ATP and polyethylene
RT glycol-stimulated topoisomerase from Sulfolobus acidocaldarius.";
RL EMBO J. 4:2123-2128(1985).
RN [6]
RP FUNCTION AS A REVERSE GYRASE, FUNCTION AS A TOPOISOMERASE, ATPASE ACTIVITY,
RP AND DNA AFFINITY.
RC STRAIN=FERM P-7137;
RX PubMed=3038879; DOI=10.1016/s0021-9258(18)60974-3;
RA Shibata T., Nakasu S., Yasui K., Kikuchi A.;
RT "Intrinsic DNA-dependent ATPase activity of reverse gyrase.";
RL J. Biol. Chem. 262:10419-10421(1987).
RN [7]
RP FUNCTION, AND SUBUNIT.
RC STRAIN=ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770;
RX PubMed=2853975; DOI=10.1021/bi00426a006;
RA Nadal M., Jaxel C., Portemer C., Forterre P., Mirambeau G., Duguet M.;
RT "Reverse gyrase of Sulfolobus: purification to homogeneity and
RT characterization.";
RL Biochemistry 27:9102-9108(1988).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP DNA-BINDING.
RX PubMed=2555155; DOI=10.1002/j.1460-2075.1989.tb08466.x;
RA Jaxel C., Nadal M., Mirambeau G., Forterre P., Takahashi M., Duguet M.;
RT "Reverse gyrase binding to DNA alters the double helix structure and
RT produces single-strand cleavage in the absence of ATP.";
RL EMBO J. 8:3135-3139(1989).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, DOMAIN, AND MUTAGENESIS OF
RP TYR-965.
RX PubMed=10748189; DOI=10.1074/jbc.m910091199;
RA Declais A.C., Marsault J., Confalonieri F., de La Tour C.B., Duguet M.;
RT "Reverse gyrase, the two domains intimately cooperate to promote positive
RT supercoiling.";
RL J. Biol. Chem. 275:19498-19504(2000).
RN [10]
RP INDUCTION.
RC STRAIN=ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770;
RX PubMed=17307872; DOI=10.1073/pnas.0611333104;
RA Lundgren M., Bernander R.;
RT "Genome-wide transcription map of an archaeal cell cycle.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2939-2944(2007).
CC -!- FUNCTION: Modifies the topological state of DNA by introducing positive
CC supercoils in an ATP-dependent process (PubMed:6328327,
CC PubMed:14708549, PubMed:3038879, PubMed:2853975, PubMed:10748189).
CC Increases the linking number in steps of +1 (PubMed:14708549). Has a
CC DNA-stimulated ATPase activity; closed circular ssDNA stimulates ATPase
CC much better than dsDNA although negative supercoiled, positive
CC supercoiled and relaxed dsDNA all stimulate ATPase activity
CC (PubMed:3038879). All NTPs permit topoisomerization (relaxation) of
CC negatively supercoiled dsDNA without nucleotide hydrolysis
CC (PubMed:3038879). It transiently cleaves a single DNA strand and
CC remains covalently bound to the 5' DNA end (PubMed:2555155). Acts via a
CC tyrosine residue (PubMed:10748189). Reverse gyrase binds and unwinds
CC DNA independently of ATP binding and DNA cleavage (PubMed:10748189).
CC May be involved in rewinding the DNA strands in the regions of the
CC chromosome that have opened up to allow transcription or replication,
CC probably acts via ssDNA regions of the chromosome (Probable).
CC {ECO:0000269|PubMed:10748189, ECO:0000269|PubMed:14708549,
CC ECO:0000269|PubMed:2555155, ECO:0000269|PubMed:2853975,
CC ECO:0000269|PubMed:3038879, ECO:0000269|PubMed:6328327,
CC ECO:0000305|PubMed:3038879}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01125, ECO:0000269|PubMed:3038879};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01125};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01125,
CC ECO:0000269|PubMed:14708549, ECO:0000269|PubMed:6328327};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Optimum temperature is 75 degrees Celsius, poor activity below 50
CC degrees Celsius (PubMed:14708549, PubMed:2555155).
CC {ECO:0000269|PubMed:14708549, ECO:0000269|PubMed:2555155};
CC -!- SUBUNIT: Monomer (PubMed:2853975). {ECO:0000255|HAMAP-Rule:MF_01125,
CC ECO:0000269|PubMed:2853975}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- INDUCTION: Constitutively transcribed during cell cycle
CC (PubMed:17307872). {ECO:0000269|PubMed:17307872}.
CC -!- DOMAIN: Introduction of positive supercoils requires the cooperation of
CC both domains (PubMed:10748189). The 2 domains can be expressed
CC separately and will reconstitute the reverse gyrase activity, neither
CC domain has the expected activity individually (PubMed:10748189). The
CC cooperative action between the helicase-like and the topoisomerase
CC domains is specific; other helicases or topoisomerases cannot
CC substitute (PubMed:10748189). The helicase-like domain probably does
CC not directly unwind DNA but acts more likely by driving ATP-dependent
CC conformational changes within the whole enzyme, functioning more like a
CC protein motor (PubMed:10748189). A beta hairpin in the 'latch' region
CC of the N-terminal domain plays a regulatory role in the enzyme,
CC repressing topoisomerase activity in the absence of ATP and therefore
CC preventing the enzyme from acting as an ATP-independent relaxing
CC enzyme; it also helps to coordinate nucleotide hydrolysis by the ATPase
CC domain with the supercoiling activity of the topoisomerase domain.
CC {ECO:0000255|HAMAP-Rule:MF_01125, ECO:0000269|PubMed:10748189}.
CC -!- PTM: The N-terminus is blocked (PubMed:8389456).
CC {ECO:0000269|PubMed:8389456}.
CC -!- MISCELLANEOUS: This enzyme is the only unique feature of
CC hyperthermophilic bacteria/archaea known and seems to be essential for
CC adaptation to life at high temperatures. It may play a role in
CC stabilization of DNA at high temperatures. {ECO:0000255|HAMAP-
CC Rule:MF_01125}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DEAD box helicase
CC family. DDVD subfamily. {ECO:0000255|HAMAP-Rule:MF_01125,
CC ECO:0000305|PubMed:8389456}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the type IA
CC topoisomerase family. {ECO:0000255|HAMAP-Rule:MF_01125}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAY80206.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; L10651; AAA72346.1; -; Genomic_DNA.
DR EMBL; CP000077; AAY80206.1; ALT_FRAME; Genomic_DNA.
DR PIR; A47445; A47445.
DR AlphaFoldDB; Q08582; -.
DR SMR; Q08582; -.
DR STRING; 330779.Saci_0839; -.
DR KEGG; sai:Saci_0839; -.
DR PATRIC; fig|330779.12.peg.804; -.
DR eggNOG; arCOG01526; Archaea.
DR HOGENOM; CLU_002886_0_0_2; -.
DR BRENDA; 5.6.2.2; 6160.
DR Proteomes; UP000001018; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004386; F:helicase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0160097; F:reverse gyrase activity; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006265; P:DNA topological change; IDA:UniProtKB.
DR GO; GO:0006268; P:DNA unwinding involved in DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd17924; DDXDc_reverse_gyrase; 1.
DR CDD; cd18798; SF2_C_reverse_gyrase; 1.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03361; TOPRIM_TopoIA_RevGyr; 1.
DR Gene3D; 2.60.510.20; -; 1.
DR Gene3D; 3.40.50.140; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 3.
DR Gene3D; 1.10.460.10; Topoisomerase I, domain 2; 1.
DR Gene3D; 1.10.290.10; Topoisomerase I, domain 4; 1.
DR HAMAP; MF_01125; Reverse_gyrase; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005736; Reverse_gyrase.
DR InterPro; IPR003601; Topo_IA_2.
DR InterPro; IPR013497; Topo_IA_cen.
DR InterPro; IPR013824; Topo_IA_cen_sub1.
DR InterPro; IPR013826; Topo_IA_cen_sub3.
DR InterPro; IPR023405; Topo_IA_core_domain.
DR InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034142; TOPRIM_RevGyr.
DR InterPro; IPR040569; Znf_Rg.
DR NCBIfam; TIGR01054; rgy; 1.
DR PANTHER; PTHR43505; REVERSE GYRASE; 1.
DR PANTHER; PTHR43505:SF1; REVERSE GYRASE; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF17915; zf_Rg; 1.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 2.
DR SUPFAM; SSF56712; Prokaryotic type I DNA topoisomerase; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS52039; TOPO_IA_2; 1.
DR PROSITE; PS50880; TOPRIM; 1.
DR PROSITE; PS52037; ZF_RG_C; 1.
DR PROSITE; PS52036; ZF_RG_N; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Cytoplasm; Direct protein sequencing; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Reference proteome;
KW Topoisomerase; Zinc; Zinc-finger.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..1248
FT /note="Reverse gyrase 1"
FT /id="PRO_0000158090"
FT DOMAIN 96..262
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 625..789
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT DOMAIN 805..1248
FT /note="Topo IA-type catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383"
FT ZN_FING 7..44
FT /note="RG N-terminal-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01380"
FT ZN_FING 706..735
FT /note="RG C-terminal-type; atypical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT REGION 621..1248
FT /note="Topoisomerase I"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT MOTIF 219..222
FT /note="DEAD box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT ACT_SITE 965
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383,
FT ECO:0000305|PubMed:10748189"
FT BINDING 16
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 19
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 34
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 37
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 92
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 109..116
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 631
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT BINDING 709
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT BINDING 713
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT BINDING 724
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT BINDING 727
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01381"
FT BINDING 758
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01125"
FT MUTAGEN 965
FT /note="Y->F: Loss of topoisomerase activity, still unwinds
FT DNA in the absence of ATP."
FT /evidence="ECO:0000269|PubMed:10748189"
SQ SEQUENCE 1248 AA; 142746 MW; 16FA5EB2F032E49A CRC64;
MQSLSDIPPS IYLFSCPNCG RSISTYRLLL GSVCNICLEE DKEYKNIGDL IKDIEKQGNL
IKLKDIQRVL DDYESFVSVF RRLLGFPPFG PQKSWIYRLL SGESFAIIAP PGLGKTTFGL
ISSIYLYLRG KKSILVFPTK SLVRQAIDKL SSYIQNLAEI KENPPKVIYY YSGMSASERK
EADEGLQSKT FDIFISTNRF LIDNIDQISS TSYQFLFVDD VDTALKSSKS AQAILKLLGF
TPSDQDKIKE SLKKYRENTQ KNEQNEYIFE EIDKIRKDRL ASKTVIFSSA TLNRSNPILT
SLVGFKPGSS VIYIRKVYDM YVKQPDKEQE TFNLIKSLLH RLGDGGLIFV PVDKKQEYIK
RLQSELSNEF NVAAITSTSA TKIDDFANGE IDVLIGSATH YGILVRGLDL PWRVKYSIFV
GIPKFKFRLG EKVNLLTLSR LLSLIALITK DQEVIYISRR VKDKIRRLSP AALTMLSVQA
KEGKLEDSIL LKAYDLLNKY LSNQNVLKRI SEIGDFVLSP DNDILIPDYL TYVQASGRTS
RIYAGDVTTG LSILLVDDFN LFRLLNKKLQ YILDDIQWRE LDVEKWTAGD VEIKNLISKI
NEERNEISKL KNEGNVAPAL QKVKTVLLVV ESPNKAKTIS SFFSRPSIRQ IGNMRVYETV
LGDKVLMVTA SGGHVYDLTT QDMGIYGVDI MKQNSSLVFI PIYNSIKKCE NNHQFTDFFE
SNKCPRCMTT KVRYDSLKSI NVLRNLAVEA DEVLIGTDPD TEGEKIAWDL YLALRPYNSN
IRRAEFHEVT RKAILQAINQ PREFNVNLVK SQLVRRIEDR WIGFKLSSIL QTRFWPEYCK
SLSSNKQLNC NENKNLSAGR VQTPVLSWIV DRYTEYQRNK SRVYYGKIDQ LQDIVIYVPK
QDGVRKNSKI VVVFNEINQL EEEFGPLPPY TTDTLLSDSN NFFGLSAPET MRIAQDLFEL
GLITYHRTDS NRISNTGISV AENYLKDVLG DKYTNIFKPR SWGDGGAHEG IRPTKPIDVE
QLRLLIEEGE LELAKRLTNN HFKVYDIIFR RFISSQIIPL KVRKEIVKIE LYGENKKEKI
NSNQNIIEVI TGITLPGIDT EISKFAYVPV RNVSRSVAER LKELGRSIPT DFSIEISNSF
IKSTVNLYTQ ADLVMEMKNK KIGRPSTYAT IIGTILRRGY VLESLKTKKL IPTRLGVEVN
KYLNENYGRF VSEDRTRKLL QLMDMVEAGQ EKYEEVLKQV YEEINEIR
//
