NICB_PSEPK
ID NICB_PSEPK Reviewed; 1187 AA.
AC Q88FX8;
DT 05-SEP-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Nicotinate dehydrogenase subunit B;
DE EC=1.17.2.1;
DE AltName: Full=Nicotinate degradation protein B;
DE AltName: Full=Nicotinate dehydrogenase large subunit;
GN Name=nicB; Synonyms=ndhL; OrderedLocusNames=PP_3948;
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=19118407; DOI=10.1007/s10532-008-9243-x;
RA Yang Y., Yuan S., Chen T., Ma P., Shang G., Dai Y.;
RT "Cloning, heterologous expression, and functional characterization of the
RT nicotinate dehydrogenase gene from Pseudomonas putida KT2440.";
RL Biodegradation 20:541-549(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=18678916; DOI=10.1073/pnas.0802273105;
RA Jimenez J.I., Canales A., Jimenez-Barbero J., Ginalski K., Rychlewski L.,
RA Garcia J.L., Diaz E.;
RT "Deciphering the genetic determinants for aerobic nicotinic acid
RT degradation: the nic cluster from Pseudomonas putida KT2440.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:11329-11334(2008).
RN [4]
RP INDUCTION.
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=21450002; DOI=10.1111/j.1462-2920.2011.02471.x;
RA Jimenez J.I., Juarez J.F., Garcia J.L., Diaz E.;
RT "A finely tuned regulatory circuit of the nicotinic acid degradation
RT pathway in Pseudomonas putida.";
RL Environ. Microbiol. 13:1718-1732(2011).
CC -!- FUNCTION: Subunit of the two-component enzyme NicAB that mediates
CC nicotinate hydroxylation, the first step in the aerobic nicotinate
CC degradation pathway. Mediates conversion of nicotinate into 6-
CC hydroxynicotinate (6HNA). {ECO:0000269|PubMed:18678916,
CC ECO:0000269|PubMed:19118407}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 Fe(III)-[cytochrome] + H2O + nicotinate = 6-
CC hydroxynicotinate + 2 Fe(II)-[cytochrome] + 2 H(+);
CC Xref=Rhea:RHEA:27417, Rhea:RHEA-COMP:11777, Rhea:RHEA-COMP:11778,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29033,
CC ChEBI:CHEBI:29034, ChEBI:CHEBI:32544, ChEBI:CHEBI:57664; EC=1.17.2.1;
CC Evidence={ECO:0000269|PubMed:18678916};
CC -!- COFACTOR:
CC Name=Mo-molybdopterin cytosine dinucleotide; Xref=ChEBI:CHEBI:71308;
CC Evidence={ECO:0000250};
CC Note=Binds 1 Mo-molybdopterin cytosine dinucleotide (Mo-MCD) cofactor
CC per subunit. {ECO:0000250};
CC -!- PATHWAY: Cofactor degradation; nicotinate degradation.
CC {ECO:0000269|PubMed:18678916}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- INDUCTION: Repressed by NicS in the absence of 6-hydroxynicotinate
CC (6HNA) or nicotinate inducers. In presence of 6HNA, repression is
CC alleviated. {ECO:0000269|PubMed:21450002}.
CC -!- DOMAIN: The cytochrome c domains probably enable interaction with the
CC electron transfer chain, possibly by delivering the electrons to a
CC cytochrome oxidase. {ECO:0000269|PubMed:18678916}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking both nicA and nicB lack the ability
CC to hydroxylate nicotinate. Cells do not grow in a nicotinate medium but
CC grow in a 6-hydroxynicotinate medium. {ECO:0000269|PubMed:18678916,
CC ECO:0000269|PubMed:19118407}.
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DR EMBL; EU604833; ACC64340.1; -; Genomic_DNA.
DR EMBL; AE015451; AAN69542.1; -; Genomic_DNA.
DR RefSeq; NP_746078.1; NC_002947.4.
DR RefSeq; WP_010954765.1; NC_002947.4.
DR AlphaFoldDB; Q88FX8; -.
DR SMR; Q88FX8; -.
DR STRING; 160488.PP_3948; -.
DR EnsemblBacteria; AAN69542; AAN69542; PP_3948.
DR KEGG; ppu:PP_3948; -.
DR PATRIC; fig|160488.4.peg.4204; -.
DR eggNOG; COG1529; Bacteria.
DR eggNOG; COG2010; Bacteria.
DR HOGENOM; CLU_007015_1_0_6; -.
DR OMA; WSAWVAD; -.
DR PhylomeDB; Q88FX8; -.
DR BioCyc; MetaCyc:G1G01-4213-MON; -.
DR BioCyc; PPUT160488:G1G01-4213-MON; -.
DR BRENDA; 1.17.1.5; 5092.
DR BRENDA; 1.17.2.1; 5092.
DR UniPathway; UPA01010; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016725; F:oxidoreductase activity, acting on CH or CH2 groups; IDA:UniProtKB.
DR GO; GO:0019439; P:aromatic compound catabolic process; IDA:UniProtKB.
DR Gene3D; 1.10.760.10; -; 3.
DR InterPro; IPR000674; Ald_Oxase/Xan_DH_a/b.
DR InterPro; IPR036856; Ald_Oxase/Xan_DH_a/b_sf.
DR InterPro; IPR008274; AldOxase/xan_DH_Mopterin-bd.
DR InterPro; IPR037165; AldOxase/xan_DH_Mopterin-bd_sf.
DR InterPro; IPR009056; Cyt_c-like_dom.
DR InterPro; IPR036909; Cyt_c-like_dom_sf.
DR Pfam; PF02738; Ald_Xan_dh_C2; 3.
DR Pfam; PF00034; Cytochrom_C; 1.
DR Pfam; PF13442; Cytochrome_CBB3; 1.
DR SMART; SM01008; Ald_Xan_dh_C; 1.
DR SUPFAM; SSF46626; SSF46626; 3.
DR SUPFAM; SSF54665; SSF54665; 1.
DR SUPFAM; SSF56003; SSF56003; 2.
DR PROSITE; PS51007; CYTC; 3.
PE 1: Evidence at protein level;
KW Aromatic hydrocarbons catabolism; Heme; Iron; Membrane; Metal-binding;
KW Molybdenum; Oxidoreductase; Reference proteome; Repeat; Transmembrane;
KW Transmembrane helix.
FT CHAIN 1..1187
FT /note="Nicotinate dehydrogenase subunit B"
FT /id="PRO_0000418465"
FT TRANSMEM 764..784
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 804..907
FT /note="Cytochrome c 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT DOMAIN 949..1057
FT /note="Cytochrome c 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT DOMAIN 1075..1163
FT /note="Cytochrome c 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 818
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 821
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 822
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 964
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 967
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 968
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 1088
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 1091
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT BINDING 1092
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
SQ SEQUENCE 1187 AA; 127875 MW; A237F711DB6CE4E5 CRC64;
MNHSQQVPSR DQLLAKTGVL LIVDQITPPS GPVAKGVTPT VKERELALFI AVSDDGMVYA
FNGHVDLGTG IRTSLAQIVA EELDLRMDQV HMVLGDTERA PNQGATIASA TLQISAVPLR
KAAATARRYL LQQAALRLGC PPEMLRIEDG TVIASNGSTL SFAELVQGKN HQLHIADDAP
LKAIEDYRLV GRSAPRVDIP GKATGELTYV HDMRLPNMLH GRVIRPPYAG HDSGDFVGNS
LLAVDESSIA HLPGVVAVVV IRDFVGVVAE REEQAIRAAH ELKVSWKPFT GKLPDLSDVA
QAIRDNPRVQ RTVLDQGDVD GGIANASQRL SRSYLWPYQL HASIGPSCAL ADFTAGQIRV
WSGTQNPHLL RADLAWLLAC DEARIEIIRM EAAGCYGRNC ADDVCADAVL LSRAVQRPVR
VQLTREQEHV WEPKGTAQLM EIDGGLNADG SVAAYDFQTS YPSNGAPTLA LLLTGAVEPV
PALFEMGDRT SIPPYDYEHM RVTINDMTPL VRASWMRGVS AMPNSFAHES YIDELAFAAG
VDPVEYRLKH LSDPRAIDLV KATAERAQWQ PHTRPMQTQA EGDVLRGRGF AYARYIHSKF
PGFGAAWAAW VADVAVDRRT GEVAVTRVVI GHDAGMMVNP EGVRHQIHGN VIQSTSRVLK
EQVSFEESTV ASKEWGGYPI LTFPELPAID VMMLPRQHEP PMGSGESASV PSAAAIANAI
FDATGIRFRE LPITAERVRA ALGGEGQGPD APAPAQPSTK RSKWWFGSLA GVFGAALGML
ATALPWRAEI APVTPPGVGS WSAAMLERGR QVAAAGDCAV CHTVSGGKAN AGGLAMDTPF
GTLYSTNITP DPETGIGRWS FAAFERAMRE GISRDGRHLY PAFPYTSFRN INDADMQALY
AYLMSQTPVR QEAPANQMRF PFNQRPLMAG WNARFLQRGE YQPDPQRSAQ WNRGAYLVDG
LGHCTACHSP RNLMGAEKGG SSYLAGGMVD GWEAPALNAL GKSSTPWSED ELFNYLSTGF
SEKHGVAAGP MGPVVSELAT LPKSDVRAIA HYLSSLEGEP QALAANAAPQ VDTHVSLSNG
ERVFKGACLG CHSDGLGPKL FGVSPSMAVN SNVHSDLPDN LLRVVLHGIP TPATRDLGYM
PGFKDSLSDR QVADLAAYLR HRFAADKPAW QGLASKAAQV RANPGSH
