NIAR_THEMA
ID NIAR_THEMA Reviewed; 175 AA.
AC Q9X1T8;
DT 31-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Probable transcription repressor NiaR;
GN Name=niaR; OrderedLocusNames=TM_1602;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP DNA-BINDING.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=18276644; DOI=10.1093/nar/gkn046;
RA Rodionov D.A., Li X., Rodionova I.A., Yang C., Sorci L., Dervyn E.,
RA Martynowski D., Zhang H., Gelfand M.S., Osterman A.L.;
RT "Transcriptional regulation of NAD metabolism in bacteria: genomic
RT reconstruction of NiaR (YrxA) regulon.";
RL Nucleic Acids Res. 36:2032-2046(2008).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH NICKEL, AND SUBUNIT.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=17256761; DOI=10.1002/prot.21221;
RA Weekes D., Miller M.D., Krishna S.S., McMullan D., McPhillips T.M.,
RA Acosta C., Canaves J.M., Elsliger M.A., Floyd R., Grzechnik S.K.,
RA Jaroszewski L., Klock H.E., Koesema E., Kovarik J.S., Kreusch A.,
RA Morse A.T., Quijano K., Spraggon G., van den Bedem H., Wolf G.,
RA Hodgson K.O., Wooley J., Deacon A.M., Godzik A., Lesley S.A., Wilson I.A.;
RT "Crystal structure of a transcription regulator (TM1602) from Thermotoga
RT maritima at 2.3 A resolution.";
RL Proteins 67:247-252(2007).
CC -!- FUNCTION: Probably functions to regulate transcription of NAD metabolic
CC genes. Binds to DNA upstream of the probable nadBII/nadA/nadC and niaRP
CC operons in a nicotinic acid dependent fashion. Nicotinic acid may be a
CC corepressor.
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Note=Binds 1 Ni(2+) ion per monomer; it is not certain this is the
CC physiological metal.;
CC -!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:17256761}.
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DR EMBL; AE000512; AAD36669.1; -; Genomic_DNA.
DR PIR; F72234; F72234.
DR RefSeq; NP_229402.1; NC_000853.1.
DR RefSeq; WP_004082049.1; NZ_CP011107.1.
DR PDB; 1J5Y; X-ray; 2.30 A; A=1-175.
DR PDBsum; 1J5Y; -.
DR AlphaFoldDB; Q9X1T8; -.
DR SMR; Q9X1T8; -.
DR STRING; 243274.THEMA_06240; -.
DR EnsemblBacteria; AAD36669; AAD36669; TM_1602.
DR KEGG; tma:TM1602; -.
DR KEGG; tmw:THMA_1642; -.
DR PATRIC; fig|243274.18.peg.1208; -.
DR eggNOG; COG1827; Bacteria.
DR InParanoid; Q9X1T8; -.
DR OMA; HTPEQTK; -.
DR OrthoDB; 1652220at2; -.
DR EvolutionaryTrace; Q9X1T8; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0036094; F:small molecule binding; IEA:InterPro.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 3.30.1340.20; -; 1.
DR InterPro; IPR035922; 3H_dom_sf.
DR InterPro; IPR004173; 3H_domain.
DR InterPro; IPR013196; HTH_11.
DR InterPro; IPR026043; NadR.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR PANTHER; PTHR40068; PTHR40068; 1.
DR Pfam; PF02829; 3H; 1.
DR Pfam; PF08279; HTH_11; 1.
DR PIRSF; PIRSF037847; NiaR; 1.
DR SUPFAM; SSF46785; SSF46785; 1.
DR SUPFAM; SSF75500; SSF75500; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Metal-binding; Nickel; Reference proteome;
KW Repressor; Transcription; Transcription regulation.
FT CHAIN 1..175
FT /note="Probable transcription repressor NiaR"
FT /id="PRO_0000409021"
FT BINDING 79
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:17256761"
FT BINDING 87
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:17256761"
FT BINDING 146
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:17256761"
FT BINDING 148
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:17256761"
FT HELIX 4..20
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 27..34
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 38..51
FT /evidence="ECO:0007829|PDB:1J5Y"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:1J5Y"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:1J5Y"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:1J5Y"
FT STRAND 70..78
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 81..83
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 84..93
FT /evidence="ECO:0007829|PDB:1J5Y"
FT STRAND 97..105
FT /evidence="ECO:0007829|PDB:1J5Y"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:1J5Y"
FT STRAND 109..117
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 120..132
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 141..144
FT /evidence="ECO:0007829|PDB:1J5Y"
FT STRAND 145..154
FT /evidence="ECO:0007829|PDB:1J5Y"
FT HELIX 155..167
FT /evidence="ECO:0007829|PDB:1J5Y"
SQ SEQUENCE 175 AA; 19555 MW; 742C3C0DF51FE8A2 CRC64;
MHMKTVRQER LKSIVRILER SKEPVSGAQL AEELSVSRQV IVQDIAYLRS LGYNIVATPR
GYVLAGGKSG VSRLVAVKHA PEEIKEELLC VVRNGGRIVD VIVEHPVYGE IRGIIDVSSE
EEVLKFVNLM EMAKTEPLLT LSGGVHLHTI EAPDEETMER IMRELKKKGF LIEEG
