RECDL_DEIRA
ID RECDL_DEIRA Reviewed; 715 AA.
AC Q9RT63;
DT 19-FEB-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=ATP-dependent RecD-like DNA helicase {ECO:0000255|HAMAP-Rule:MF_01488};
DE EC=3.6.4.12 {ECO:0000255|HAMAP-Rule:MF_01488};
GN Name=recD2 {ECO:0000255|HAMAP-Rule:MF_01488}; OrderedLocusNames=DR_1902;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP FUNCTION AS AN ATPASE, FUNCTION AS A HELICASE, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND DNA-BINDING.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=15466873; DOI=10.1074/jbc.m408645200;
RA Wang J., Julin D.A.;
RT "DNA helicase activity of the RecD protein from Deinococcus radiodurans.";
RL J. Biol. Chem. 279:52024-52032(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 151-715, AND MUTAGENESIS OF
RP 412-LEU--PHE-419.
RX PubMed=18668125; DOI=10.1038/emboj.2008.144;
RA Saikrishnan K., Griffiths S.P., Cook N., Court R., Wigley D.B.;
RT "DNA binding to RecD: role of the 1B domain in SF1B helicase activity.";
RL EMBO J. 27:2222-2229(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 151-715 IN COMPLEX WITH DNA AND
RP ATP, FUNCTION, MECHANISM, AND MUTAGENESIS OF ASN-596; TYR-598 AND ASN-604.
RX PubMed=19490894; DOI=10.1016/j.cell.2009.03.036;
RA Saikrishnan K., Powell B., Cook N.J., Webb M.R., Wigley D.B.;
RT "Mechanistic basis of 5'-3' translocation in SF1B helicases.";
RL Cell 137:849-859(2009).
CC -!- FUNCTION: DNA-dependent ATPase (ssDNA better than dsDNA) and ATP-
CC dependent 5'-3' DNA helicase. Appears to move along DNA in single base
CC steps, powered by hydrolysis of 1 molecule of ATP. Has low
CC processivity; short (20 bp) substrates with 5'-overhangs or forked ends
CC are the best substrates, is much less efficient on 52 or 76 bp
CC substrates with 5'- overhangs. The presence of single-stranded DNA-
CC binding protein (SSB) increases unwinding 4-5 fold. Has no activity on
CC blunt DNA or DNA with 3'-overhangs. Requires at least 10 bases of 5'-
CC ssDNA for helicase activity. {ECO:0000269|PubMed:15466873,
CC ECO:0000269|PubMed:19490894}.
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; EC=3.6.4.12;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01488};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.3 to 6.5 for unwinding of a 56 bp substrate and DNA
CC hairpin binding. {ECO:0000269|PubMed:15466873};
CC -!- MISCELLANEOUS: There are no RecB or RecC orthologs in this organism.
CC -!- SIMILARITY: Belongs to the RecD family. RecD-like subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01488}.
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DR EMBL; AE000513; AAF11453.1; -; Genomic_DNA.
DR PIR; G75339; G75339.
DR RefSeq; NP_295625.1; NC_001263.1.
DR RefSeq; WP_010888537.1; NZ_CP015081.1.
DR PDB; 3E1S; X-ray; 2.20 A; A=151-715.
DR PDB; 3GP8; X-ray; 2.50 A; A=151-715.
DR PDB; 3GPL; X-ray; 2.50 A; A/B=151-715.
DR PDBsum; 3E1S; -.
DR PDBsum; 3GP8; -.
DR PDBsum; 3GPL; -.
DR AlphaFoldDB; Q9RT63; -.
DR SMR; Q9RT63; -.
DR STRING; 243230.DR_1902; -.
DR EnsemblBacteria; AAF11453; AAF11453; DR_1902.
DR KEGG; dra:DR_1902; -.
DR PATRIC; fig|243230.17.peg.2117; -.
DR eggNOG; COG0507; Bacteria.
DR HOGENOM; CLU_007524_0_3_0; -.
DR InParanoid; Q9RT63; -.
DR OMA; SHPQYGR; -.
DR OrthoDB; 961809at2; -.
DR BRENDA; 3.6.4.12; 1856.
DR EvolutionaryTrace; Q9RT63; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0009338; C:exodeoxyribonuclease V complex; IBA:GO_Central.
DR GO; GO:0043139; F:5'-3' DNA helicase activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0008094; F:ATP-dependent activity, acting on DNA; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR GO; GO:0017116; F:single-stranded DNA helicase activity; IBA:GO_Central.
DR GO; GO:0006310; P:DNA recombination; IBA:GO_Central.
DR Gene3D; 3.40.50.300; -; 2.
DR HAMAP; MF_01488; RecD_like; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR006345; DNA_helicase_RecD-like.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR029493; RecD-like_HHH.
DR InterPro; IPR041451; RecD-like_SH13.
DR InterPro; IPR027785; UvrD-like_helicase_C.
DR Pfam; PF14490; HHH_4; 1.
DR Pfam; PF18335; SH3_13; 1.
DR Pfam; PF13538; UvrD_C_2; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR TIGRFAMs; TIGR01448; recD_rel; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA-binding; Helicase; Hydrolase;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..715
FT /note="ATP-dependent RecD-like DNA helicase"
FT /id="PRO_0000425413"
FT DNA_BIND 391
FT DNA_BIND 407..414
FT DNA_BIND 470
FT DNA_BIND 554..555
FT DNA_BIND 596..604
FT DNA_BIND 644..647
FT REGION 1..150
FT /note="Not required for helicase activity"
FT BINDING 343
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:19490894"
FT BINDING 363..367
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01488,
FT ECO:0000269|PubMed:19490894"
FT BINDING 466
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:19490894"
FT BINDING 493
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:19490894"
FT BINDING 679
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:19490894"
FT MUTAGEN 412..419
FT /note="LGYGPQGF->G: Loss of helicase, little effect on DNA-
FT binding or DNA-dependent ATPase."
FT /evidence="ECO:0000269|PubMed:18668125"
FT MUTAGEN 596
FT /note="N->A: Loss of helicase."
FT /evidence="ECO:0000269|PubMed:19490894"
FT MUTAGEN 598
FT /note="Y->A: Loss of helicase."
FT /evidence="ECO:0000269|PubMed:19490894"
FT MUTAGEN 604
FT /note="N->A: 10-fold reduction in helicase."
FT /evidence="ECO:0000269|PubMed:19490894"
FT HELIX 157..165
FT /evidence="ECO:0007829|PDB:3GP8"
FT HELIX 170..180
FT /evidence="ECO:0007829|PDB:3GP8"
FT HELIX 184..190
FT /evidence="ECO:0007829|PDB:3GP8"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 203..207
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 220..237
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 245..256
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 260..272
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 275..279
FT /evidence="ECO:0007829|PDB:3E1S"
FT TURN 288..292
FT /evidence="ECO:0007829|PDB:3GP8"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 299..317
FT /evidence="ECO:0007829|PDB:3E1S"
FT TURN 333..338
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 341..350
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 354..359
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 366..379
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 384..390
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 391..401
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 405..407
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 408..411
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 418..420
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 422..425
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 430..434
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 437..439
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 442..449
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 457..462
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 470..472
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 475..482
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 485..487
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 493..496
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 499..508
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 520..524
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 531..540
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 544..546
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 548..552
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 554..556
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 560..571
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 581..585
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 590..593
FT /evidence="ECO:0007829|PDB:3E1S"
FT TURN 598..601
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 607..613
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 618..622
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 625..629
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 631..634
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 637..639
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 641..644
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 645..648
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 653..660
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 662..667
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 670..678
FT /evidence="ECO:0007829|PDB:3E1S"
FT STRAND 680..688
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 690..698
FT /evidence="ECO:0007829|PDB:3E1S"
FT HELIX 708..715
FT /evidence="ECO:0007829|PDB:3E1S"
SQ SEQUENCE 715 AA; 76431 MW; 6FBCAB24474EA99B CRC64;
MSAALPAEPF RVSGGVNKVR FRSDTGFTVM SATLRNEQGE DPDATVIGVM PPLDVGDTFS
AEVLMEEHRE YGYQYRVVNM VLEAMPADLS EEGVAAYFEA RVGGVGKVLA GRIAKTFGAA
AFDLLEDDPQ KFLQVPGITE STLHKMVSSW SQQGLERRLL AGLQGLGLTI NQAQRAVKHF
GADALDRLEK DLFTLTEVEG IGFLTADKLW QARGGALDDP RRLTAAAVYA LQLAGTQAGH
SFLPRSRAEK GVVHYTRVTP GQARLAVETA VELGRLSEDD SPLFAAEAAA TGEGRIYLPH
VLRAEKKLAS LIRTLLATPP ADGAGNDDWA VPKKARKGLS EEQASVLDQL AGHRLVVLTG
GPGTGKSTTT KAVADLAESL GLEVGLCAPT GKAARRLGEV TGRTASTVHR LLGYGPQGFR
HNHLEPAPYD LLIVDEVSMM GDALMLSLLA AVPPGARVLL VGDTDQLPPV DAGLPLLALA
QAAPTIKLTQ VYRQAAKNPI IQAAHGLLHG EAPAWGDKRL NLTEIEPDGG ARRVALMVRE
LGGPGAVQVL TPMRKGPLGM DHLNYHLQAL FNPGEGGVRI AEGEARPGDT VVQTKNDYNN
EIFNGTLGMV LKAEGARLTV DFDGNVVELT GAELFNLQLG YALTVHRAQG SEWGTVLGVL
HEAHMPMLSR NLVYTALTRA RDRFFSAGSA SAWQIAAARQ REARNTALLE RIRAH
