RIR2_AQUAE
ID RIR2_AQUAE Reviewed; 696 AA.
AC O67475;
DT 26-SEP-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit beta;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase small subunit;
DE Contains:
DE RecName: Full=Aae NrdB intein;
DE AltName: Full=Aae RIR2 intein;
GN Name=nrdB; OrderedLocusNames=aq_1505;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-
CC diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:23252, Rhea:RHEA-COMP:10698, Rhea:RHEA-
CC COMP:10700, ChEBI:CHEBI:15377, ChEBI:CHEBI:29950, ChEBI:CHEBI:50058,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:73316; EC=1.17.4.1;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU10014};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875; Evidence={ECO:0000250};
CC Note=Binds 2 iron ions per subunit. {ECO:0000250};
CC -!- PATHWAY: Genetic information processing; DNA replication.
CC -!- SUBUNIT: Tetramer of two alpha and two beta subunits. {ECO:0000250}.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase small
CC chain family. {ECO:0000305}.
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DR EMBL; AE000657; AAC07431.1; -; Genomic_DNA.
DR PIR; A70431; A70431.
DR RefSeq; NP_214040.1; NC_000918.1.
DR RefSeq; WP_010880978.1; NC_000918.1.
DR PDB; 7AIK; X-ray; 2.10 A; A=7-232.
DR PDB; 7AIL; X-ray; 1.73 A; A=1-696.
DR PDBsum; 7AIK; -.
DR PDBsum; 7AIL; -.
DR AlphaFoldDB; O67475; -.
DR SMR; O67475; -.
DR STRING; 224324.aq_1505; -.
DR EnsemblBacteria; AAC07431; AAC07431; aq_1505.
DR KEGG; aae:aq_1505; -.
DR PATRIC; fig|224324.8.peg.1175; -.
DR eggNOG; COG0208; Bacteria.
DR eggNOG; COG1372; Bacteria.
DR HOGENOM; CLU_395702_0_0_0; -.
DR InParanoid; O67475; -.
DR OrthoDB; 1384440at2; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000000798; Chromosome.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IEA:InterPro.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR CDD; cd01049; RNRR2; 1.
DR Gene3D; 1.10.620.20; -; 2.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR012348; RNR-like.
DR InterPro; IPR033909; RNR_small.
DR InterPro; IPR030475; RNR_small_AS.
DR InterPro; IPR000358; RNR_small_fam.
DR PANTHER; PTHR23409; PTHR23409; 1.
DR Pfam; PF00268; Ribonuc_red_sm; 2.
DR SMART; SM00306; HintN; 1.
DR SUPFAM; SSF47240; SSF47240; 2.
DR SUPFAM; SSF51294; SSF51294; 1.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
DR PROSITE; PS00368; RIBORED_SMALL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Autocatalytic cleavage; Deoxyribonucleotide synthesis;
KW Endonuclease; Hydrolase; Intron homing; Iron; Metal-binding; Nuclease;
KW Oxidoreductase; Protein splicing; Reference proteome.
FT CHAIN 1..229
FT /note="Ribonucleoside-diphosphate reductase subunit beta,
FT 1st part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000030598"
FT CHAIN 230..575
FT /note="Aae NrdB intein"
FT /evidence="ECO:0000255"
FT /id="PRO_0000030599"
FT CHAIN 576..696
FT /note="Ribonucleoside-diphosphate reductase subunit beta,
FT 2nd part"
FT /evidence="ECO:0000255"
FT /id="PRO_0000030600"
FT DOMAIN 377..507
FT /note="DOD-type homing endonuclease"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00273"
FT ACT_SITE 134
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 97
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 127
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 127
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 130
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT BINDING 194
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 228
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 577
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT HELIX 23..25
FT /evidence="ECO:0007829|PDB:7AIL"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 45..55
FT /evidence="ECO:0007829|PDB:7AIL"
FT TURN 56..58
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 70..76
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 80..110
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 114..141
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 144..151
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 158..176
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 180..196
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 199..210
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 215..230
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 577..591
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 593..595
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 598..623
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 632..648
FT /evidence="ECO:0007829|PDB:7AIL"
FT TURN 649..651
FT /evidence="ECO:0007829|PDB:7AIL"
FT TURN 663..666
FT /evidence="ECO:0007829|PDB:7AIL"
FT HELIX 667..670
FT /evidence="ECO:0007829|PDB:7AIL"
SQ SEQUENCE 696 AA; 82931 MW; E5929D55C455A5EB CRC64;
MEKTEKNELV RKLIFNPQGD REASKRKIIK GNPTNIFELN EIKYSWAFDL YKLMGFTNFW
IPEEIQMLED RKQYETVLSD YEKRAYELVL SFLIALDSFQ VDMLKEFGRM ITAPEVEMAI
TAQEFQESVH AYSYQFILES VVDPVKADEI YNYWREDERL LERNKVIAEL YNEFIRKPNE
ENFIKATIGN YILESLYFYS GFAFFYTLGR QGKMRNTVQQ IKYINRDELC FIEGTEVLTK
RGFVDFRELR EDDLVAQYDI ETGEISWTKP YAYVERDYEG SMYRLKHPKS NWEVVATEGH
EFIVRNLKTG KERKEPIEKV KLHPYSAIPV AGRYTGEVEE YDLWELVSGK GITLKTRSAV
KNKLTPIEKL LIVLQADGTI DSKRNGKFTG FQQLKFFFSK YRKINEFEKI LNECAPYGIK
WKKYERQDGI AYTVYYPNDL PIKPTKFFDE WVRLDEITEE WIREFVEELV KWDGHIPKDR
NKKKVYYYST KEKRNKDFVQ ALCALGGMRT VVSRERNPKA KNPVYRIWIY LEDDYINTQT
MVKEEFYYKG KVYCVSVPKG NIVVRYKDSV CIAGNCHVTL FRNIINTLRK ENPELFTPEI
EKWIVEYFKY AVNEEIKWGQ YVTQNQILGI NDVLIERYIK YLGNLRITQI GFDPIYPEVT
ENPLKWIDEF RKINNTKTDF FQAKPQTYSK ANELKW
