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   27-MAR-2024, entry version 146.
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; Aquificota; 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   -!- 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; 9766544at2; -.
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:UniProtKB-KW.
DR   GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR   GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR   CDD; cd00081; Hint; 1.
DR   CDD; cd01049; RNRR2; 1.
DR   Gene3D; 1.10.620.20; Ribonucleotide Reductase, subunit A; 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   NCBIfam; TIGR01443; intein_Cterm; 1.
DR   NCBIfam; TIGR01445; intein_Nterm; 1.
DR   PANTHER; PTHR23409; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN; 1.
DR   PANTHER; PTHR23409:SF18; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2; 1.
DR   Pfam; PF00268; Ribonuc_red_sm; 2.
DR   SMART; SM00306; HintN; 1.
DR   SUPFAM; SSF47240; Ferritin-like; 2.
DR   SUPFAM; SSF51294; Hedgehog/intein (Hint) domain; 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
//