HJC_PYRFU
ID HJC_PYRFU Reviewed; 123 AA.
AC E7FHX4; Q7LWY2; Q9V301;
DT 14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 1.
DT 03-AUG-2022, entry version 70.
DE RecName: Full=Holliday junction resolvase Hjc {ECO:0000255|HAMAP-Rule:MF_01490};
DE Short=Hjc {ECO:0000255|HAMAP-Rule:MF_01490};
DE EC=3.1.21.10 {ECO:0000255|HAMAP-Rule:MF_01490};
GN Name=hjc {ECO:0000255|HAMAP-Rule:MF_01490}; OrderedLocusNames=PF1503;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS A HOLLIDAY JUNCTION
RP ENDONUCLEASE, INTERACTION WITH PCNA, SUBUNIT, AND DNA-BINDING.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430863; DOI=10.1073/pnas.96.16.8873;
RA Komori K., Sakae S., Shinagawa H., Morikawa K., Ishino Y.;
RT "A Holliday junction resolvase from Pyrococcus furiosus: functional
RT similarity to Escherichia coli RuvC provides evidence for conserved
RT mechanism of homologous recombination in Bacteria, Eukarya, and Archaea.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:8873-8878(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [3]
RP ACTIVITY REGULATION, INTERACTION WITH RADB, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10903318; DOI=10.1074/jbc.m004557200;
RA Komori K., Miyata T., DiRuggiero J., Holley-Shanks R., Hayashi I.,
RA Cann I.K.O., Mayanagi K., Shinagawa H., Ishino Y.;
RT "Both RadA and RadB are involved in homologous recombination in Pyrococcus
RT furiosus.";
RL J. Biol. Chem. 275:33782-33790(2000).
RN [4]
RP FUNCTION, SUBUNIT, DNA-BINDING, AND MUTAGENESIS OF GLU-9; ARG-10; GLU-11;
RP PHE-21; ARG-25; ASP-33; GLU-46; LYS-48; TYR-56; PHE-68; PHE-72; LYS-81;
RP PHE-89 AND GLU-110.
RX PubMed=11005813; DOI=10.1074/jbc.m006294200;
RA Komori K., Sakae S., Daiyasu H., Toh H., Morikawa K., Shinagawa H.,
RA Ishino Y.;
RT "Mutational analysis of the Pyrococcus furiosus holliday junction resolvase
RT hjc revealed functionally important residues for dimer formation, junction
RT DNA binding, and cleavage activities.";
RL J. Biol. Chem. 275:40385-40391(2000).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
RP DNA-BINDING.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=11071944; DOI=10.1093/nar/28.22.4544;
RA Komori K., Sakae S., Fujikane R., Morikawa K., Shinagawa H., Ishino Y.;
RT "Biochemical characterization of the hjc holliday junction resolvase of
RT Pyrococcus furiosus.";
RL Nucleic Acids Res. 28:4544-4551(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS), SUBUNIT, AND MUTAGENESIS OF
RP 3-ARG-LYS-4 AND ASP-33.
RX PubMed=11441015; DOI=10.1074/jbc.m104460200;
RA Nishino T., Komori K., Ishino Y., Morikawa K.;
RT "Dissection of the regional roles of the archaeal Holliday junction
RT resolvase Hjc by structural and mutational analyses.";
RL J. Biol. Chem. 276:35735-35740(2001).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS), SUBUNIT, AND MUTAGENESIS OF
RP 1-MET--GLY-5; 30-LYS-LYS-31 AND 51-LYS-LYS-52.
RX PubMed=11286886; DOI=10.1016/s0969-2126(01)00576-7;
RA Nishino T., Komori K., Tsuchiya D., Ishino Y., Morikawa K.;
RT "Crystal structure of the archaeal holliday junction resolvase Hjc and
RT implications for DNA recognition.";
RL Structure 9:197-204(2001).
CC -!- FUNCTION: A structure-specific endonuclease that resolves Holliday
CC junction (HJ) intermediates during genetic recombination. Cleaves 4-way
CC DNA junctions introducing paired nicks in opposing strands, leaving a
CC 5'-terminal phosphate and a 3'-terminal hydroxyl group that are ligated
CC to produce recombinant products. Cleaves both mobile and immobile
CC junctions. Binds 4-way junction DNA, a synthetic Hj, binding is not
CC competed by dsDNA. {ECO:0000255|HAMAP-Rule:MF_01490,
CC ECO:0000269|PubMed:10430863, ECO:0000269|PubMed:11005813,
CC ECO:0000269|PubMed:11071944}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage at a junction such as a reciprocal
CC single-stranded crossover between two homologous DNA duplexes
CC (Holliday junction).; EC=3.1.21.10; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01490, ECO:0000269|PubMed:11071944};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11071944};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:11071944};
CC Note=Divalent cations, Mg(2+) has higher activity than Mn(2+).
CC {ECO:0000269|PubMed:11071944};
CC -!- ACTIVITY REGULATION: Cleavage inhibited by RadB in the absence (but not
CC presence) of ATP. {ECO:0000269|PubMed:10903318}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8-10. {ECO:0000269|PubMed:11071944};
CC Temperature dependence:
CC Optimum temperature is 70-75 degrees Celsius, enzyme is fully active
CC after 16 hours at 90 degrees Celsius. {ECO:0000269|PubMed:11071944};
CC -!- SUBUNIT: Homodimer. Probably interacts with PCNA and RadB.
CC {ECO:0000255|HAMAP-Rule:MF_01490, ECO:0000269|PubMed:10430863,
CC ECO:0000269|PubMed:10903318, ECO:0000269|PubMed:11005813,
CC ECO:0000269|PubMed:11286886, ECO:0000269|PubMed:11441015}.
CC -!- SIMILARITY: Belongs to the Holliday junction resolvase Hjc family.
CC {ECO:0000255|HAMAP-Rule:MF_01490}.
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DR EMBL; AB023635; BAA82839.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL81627.1; -; Genomic_DNA.
DR RefSeq; WP_011012650.1; NC_018092.1.
DR PDB; 1GEF; X-ray; 2.00 A; A/B/D/E=1-123.
DR PDB; 1IPI; X-ray; 2.16 A; A/B=1-123.
DR PDBsum; 1GEF; -.
DR PDBsum; 1IPI; -.
DR AlphaFoldDB; E7FHX4; -.
DR SMR; E7FHX4; -.
DR STRING; 186497.PF1503; -.
DR EnsemblBacteria; AAL81627; AAL81627; PF1503.
DR GeneID; 41713321; -.
DR KEGG; pfu:PF1503; -.
DR PATRIC; fig|186497.12.peg.1566; -.
DR eggNOG; arCOG00919; Archaea.
DR HOGENOM; CLU_139546_2_0_2; -.
DR OMA; WYFFHPG; -.
DR PhylomeDB; E7FHX4; -.
DR BRENDA; 3.1.21.10; 5243.
DR EvolutionaryTrace; E7FHX4; -.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0048476; C:Holliday junction resolvase complex; IMP:CACAO.
DR GO; GO:0008821; F:crossover junction endodeoxyribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR CDD; cd00523; archeal_HJR; 1.
DR Gene3D; 3.40.1350.10; -; 1.
DR HAMAP; MF_01490; HJ_Resolv_Hjc; 1.
DR InterPro; IPR002732; Hjc.
DR InterPro; IPR014428; Hjc_arc.
DR InterPro; IPR011335; Restrct_endonuc-II-like.
DR InterPro; IPR011856; tRNA_endonuc-like_dom_sf.
DR PANTHER; PTHR39651; PTHR39651; 1.
DR Pfam; PF01870; Hjc; 1.
DR PIRSF; PIRSF004985; Hlld_jn_rslvs_ar; 1.
DR SUPFAM; SSF52980; SSF52980; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA recombination; DNA repair; DNA-binding;
KW Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Reference proteome.
FT CHAIN 1..123
FT /note="Holliday junction resolvase Hjc"
FT /id="PRO_0000429156"
FT ACT_SITE 29
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01490"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01490"
FT BINDING 33
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01490"
FT BINDING 46
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01490"
FT SITE 48
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255"
FT MUTAGEN 1..5
FT /note="Missing: No Holliday junction (HJ) cleavage, does
FT not bind HJ DNA."
FT /evidence="ECO:0000269|PubMed:11286886"
FT MUTAGEN 3..4
FT /note="RK->AA: 20-fold decrease in HJ cleavage, decreased
FT binding to HJ DNA."
FT /evidence="ECO:0000269|PubMed:11441015"
FT MUTAGEN 9
FT /note="E->A: No HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 10
FT /note="R->A: No HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 11
FT /note="E->A: Wild-type HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 21
FT /note="F->A: Wild-type HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 25
FT /note="R->A: No HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 30..31
FT /note="KK->AA: No HJ cleavage, binds HJ DNA about 50%."
FT /evidence="ECO:0000269|PubMed:11286886"
FT MUTAGEN 33
FT /note="D->A: No HJ cleavage. Binds HJ DNA normally."
FT /evidence="ECO:0000269|PubMed:11005813,
FT ECO:0000269|PubMed:11441015"
FT MUTAGEN 46
FT /note="E->A: No HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 48
FT /note="K->A: No HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 51..52
FT /note="KK->AA: 10% HJ cleavage, binds HJ DNA about 50%."
FT /evidence="ECO:0000269|PubMed:11286886"
FT MUTAGEN 56
FT /note="Y->A: 30% HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 68
FT /note="F->A: No HJ cleavage. Dimerizes poorly."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 72
FT /note="F->A: No HJ cleavage; at very high levels altered
FT cleavage patterns. Dimerizes poorly."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 81
FT /note="K->A: No HJ cleavage. Slight decrease in DNA
FT binding."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 89
FT /note="F->A: Wild-type HJ cleavage."
FT /evidence="ECO:0000269|PubMed:11005813"
FT MUTAGEN 110
FT /note="E->A: Wild-type HJ cleavage. Slight decrease in DNA
FT binding."
FT /evidence="ECO:0000269|PubMed:11005813"
FT HELIX 3..18
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 22..26
FT /evidence="ECO:0007829|PDB:1GEF"
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 42..53
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:1GEF"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 75..82
FT /evidence="ECO:0007829|PDB:1GEF"
FT TURN 83..85
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 86..91
FT /evidence="ECO:0007829|PDB:1GEF"
FT STRAND 99..101
FT /evidence="ECO:0007829|PDB:1GEF"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:1GEF"
FT HELIX 109..112
FT /evidence="ECO:0007829|PDB:1GEF"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:1GEF"
SQ SEQUENCE 123 AA; 13766 MW; 496D9D72D68A2B43 CRC64;
MYRKGAQAER ELIKLLEKHG FAVVRSAGSK KVDLVAGNGK KYLCIEVKVT KKDHLYVGKR
DMGRLIEFSR RFGGIPVLAV KFLNVGWRFI EVSPKIEKFV FTPSSGVSLE VLLGIQKTLE
GKS
