ID H6NIM5_9BACL Unreviewed; 345 AA.
AC H6NIM5;
DT 18-APR-2012, integrated into UniProtKB/TrEMBL.
DT 18-APR-2012, sequence version 1.
DT 27-MAR-2024, entry version 53.
DE RecName: Full=Ribonucleoside-diphosphate reductase subunit beta {ECO:0000256|PIRNR:PIRNR000355};
DE EC=1.17.4.1 {ECO:0000256|PIRNR:PIRNR000355};
GN ORFNames=PM3016_6464 {ECO:0000313|EMBL:AFC33092.1};
OS Paenibacillus mucilaginosus 3016.
OC Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
OX NCBI_TaxID=1116391 {ECO:0000313|EMBL:AFC33092.1, ECO:0000313|Proteomes:UP000007523};
RN [1] {ECO:0000313|EMBL:AFC33092.1, ECO:0000313|Proteomes:UP000007523}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3016 {ECO:0000313|EMBL:AFC33092.1,
RC ECO:0000313|Proteomes:UP000007523};
RX PubMed=22535950; DOI=10.1128/JB.00323-12;
RA Ma M., Wang Z., Li L., Jiang X., Guan D., Cao F., Chen H., Wang X.,
RA Shen D., Du B., Li J.;
RT "Complete Genome Sequence of Paenibacillus mucilaginosus 3016, a Bacterium
RT Functional as Microbial Fertilizer.";
RL J. Bacteriol. 194:2777-2778(2012).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. {ECO:0000256|PIRNR:PIRNR000355}.
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:0000256|PIRNR:PIRNR000355};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000256|PIRNR:PIRNR000355,
CC ECO:0000256|PIRSR:PIRSR000355-2};
CC Note=Binds 2 iron ions per subunit. {ECO:0000256|PIRNR:PIRNR000355,
CC ECO:0000256|PIRSR:PIRSR000355-2};
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase small
CC chain family. {ECO:0000256|ARBA:ARBA00009303,
CC ECO:0000256|PIRNR:PIRNR000355}.
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DR EMBL; CP003235; AFC33092.1; -; Genomic_DNA.
DR RefSeq; WP_013920514.1; NC_016935.1.
DR AlphaFoldDB; H6NIM5; -.
DR STRING; 1116391.PM3016_6464; -.
DR KEGG; pmq:PM3016_6464; -.
DR HOGENOM; CLU_035339_1_0_9; -.
DR UniPathway; UPA00326; -.
DR Proteomes; UP000007523; Chromosome.
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 CDD; cd01049; RNRR2; 1.
DR Gene3D; 1.10.620.20; Ribonucleotide Reductase, subunit A; 1.
DR InterPro; IPR009078; Ferritin-like_SF.
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; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN; 1.
DR PANTHER; PTHR23409:SF18; RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2; 1.
DR Pfam; PF00268; Ribonuc_red_sm; 1.
DR PIRSF; PIRSF000355; NrdB; 1.
DR SUPFAM; SSF47240; Ferritin-like; 1.
DR PROSITE; PS00368; RIBORED_SMALL; 1.
PE 3: Inferred from homology;
KW Deoxyribonucleotide synthesis {ECO:0000256|PIRNR:PIRNR000355};
KW Iron {ECO:0000256|PIRNR:PIRNR000355, ECO:0000256|PIRSR:PIRSR000355-2};
KW Metal-binding {ECO:0000256|PIRNR:PIRNR000355,
KW ECO:0000256|PIRSR:PIRSR000355-2};
KW Oxidoreductase {ECO:0000256|PIRNR:PIRNR000355};
KW Reference proteome {ECO:0000313|Proteomes:UP000007523}.
FT ACT_SITE 126
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-1"
FT BINDING 89
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
FT BINDING 119
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
FT BINDING 119
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
FT BINDING 122
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
FT BINDING 186
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
FT BINDING 220
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
FT BINDING 223
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR000355-2"
SQ SEQUENCE 345 AA; 41086 MW; D4235A00587BE56B CRC64;
MDLQKKKLFN ENGDRDWGKR RMIGGNTTNL IELNNVKYDW ATKMYRTMMN NFWIPEEIPL
AQDAKDYKFL SPEERQSYDK IISFLIFLDS LQTANLPNIN EYITASEVNL CLTVQTFQEA
VHSQSYSYIL DSVCSAEVRD EIYNQWREDK HLLKRNRFIT DLYERFIEEP STDNLMRTIM
ANYILEGIYF YSGFSFFYAL GRQGKMLGTV SEIKYIQRDE LTHLALFQNI FREIRKENPE
VFTDELIEDL RGMMRTAVSH EIEWGQYITN NKIHGLSNEI IDQYIKYLSN ERMRKLGLEI
LYPEIVEHPM KWVESFSNMN AIKTDFFEQK VTNYSKSSNL NWDDL
//
