LARB_LACPL
ID LARB_LACPL Reviewed; 246 AA.
AC F9UST0;
DT 27-SEP-2017, integrated into UniProtKB/Swiss-Prot.
DT 19-OCT-2011, sequence version 1.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=Pyridinium-3,5-biscarboxylic acid mononucleotide synthase {ECO:0000305|PubMed:27114550};
DE Short=P2CMN synthase {ECO:0000305|PubMed:27114550};
DE EC=2.5.1.143 {ECO:0000269|PubMed:27114550};
DE AltName: Full=Lactate racemase accessory protein LarB {ECO:0000303|PubMed:24710389};
DE AltName: Full=Lactate racemase activation protein LarB {ECO:0000303|PubMed:24710389};
DE AltName: Full=Lactate racemase maturation protein LarB {ECO:0000303|PubMed:24710389};
DE AltName: Full=Lactate racemization operon protein LarB {ECO:0000303|PubMed:16166538, ECO:0000312|EMBL:CCC77661.1};
DE AltName: Full=Nickel-pincer cofactor biosynthesis protein LarB {ECO:0000305|PubMed:27114550};
DE AltName: Full=Nicotinic acid adenine dinucleotide carboxylase/hydrolase {ECO:0000305|PubMed:27114550};
DE Short=NaAD carboxylase/hydrolase {ECO:0000305|PubMed:27114550};
GN Name=larB {ECO:0000303|PubMed:16166538, ECO:0000312|EMBL:CCC77661.1};
GN OrderedLocusNames=lp_0105 {ECO:0000312|EMBL:CCC77661.1};
OS Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
OS (Lactobacillus plantarum).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
OC Lactiplantibacillus.
OX NCBI_TaxID=220668;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
RX PubMed=12566566; DOI=10.1073/pnas.0337704100;
RA Kleerebezem M., Boekhorst J., van Kranenburg R., Molenaar D., Kuipers O.P.,
RA Leer R., Tarchini R., Peters S.A., Sandbrink H.M., Fiers M.W.E.J.,
RA Stiekema W., Klein Lankhorst R.M., Bron P.A., Hoffer S.M.,
RA Nierop Groot M.N., Kerkhoven R., De Vries M., Ursing B., De Vos W.M.,
RA Siezen R.J.;
RT "Complete genome sequence of Lactobacillus plantarum WCFS1.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:1990-1995(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME REANNOTATION.
RC STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
RX PubMed=22156394; DOI=10.1128/jb.06275-11;
RA Siezen R.J., Francke C., Renckens B., Boekhorst J., Wels M.,
RA Kleerebezem M., van Hijum S.A.;
RT "Complete resequencing and reannotation of the Lactobacillus plantarum
RT WCFS1 genome.";
RL J. Bacteriol. 194:195-196(2012).
RN [3]
RP INDUCTION.
RC STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
RX PubMed=16166538; DOI=10.1128/jb.187.19.6750-6761.2005;
RA Goffin P., Deghorain M., Mainardi J.L., Tytgat I., Champomier-Verges M.C.,
RA Kleerebezem M., Hols P.;
RT "Lactate racemization as a rescue pathway for supplying D-lactate to the
RT cell wall biosynthesis machinery in Lactobacillus plantarum.";
RL J. Bacteriol. 187:6750-6761(2005).
RN [4]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
RX PubMed=24710389; DOI=10.1038/ncomms4615;
RA Desguin B., Goffin P., Viaene E., Kleerebezem M., Martin-Diaconescu V.,
RA Maroney M.J., Declercq J.P., Soumillion P., Hols P.;
RT "Lactate racemase is a nickel-dependent enzyme activated by a widespread
RT maturation system.";
RL Nat. Commun. 5:3615-3615(2014).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=27114550; DOI=10.1073/pnas.1600486113;
RA Desguin B., Soumillion P., Hols P., Hausinger R.P.;
RT "Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium
RT carboxylation and LarE-dependent sacrificial sulfur insertion.";
RL Proc. Natl. Acad. Sci. U.S.A. 113:5598-5603(2016).
CC -!- FUNCTION: Involved in the biosynthesis of a nickel-pincer cofactor
CC ((SCS)Ni(II) pincer complex). Carboxylates the pyridinium ring of
CC nicotinic acid adenine dinucleotide (NaAD) and cleaves the
CC phosphoanhydride bond to release AMP and generate pyridinium-3,5-
CC biscarboxylic acid mononucleotide (P2CMN) (PubMed:27114550). LarB can
CC hydrolyze NaAD directly or it first forms an adduct with NaAD that
CC releases AMP and reacts with bicarbonate/CO2 to generate P2CMN
CC (PubMed:27114550). Is required for the activation of the lactate
CC racemase LarA (PubMed:24710389). May also be involved in the activation
CC of other nickel-pincer cofactor-dependent enzymes (PubMed:27114550).
CC {ECO:0000269|PubMed:24710389, ECO:0000269|PubMed:27114550}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=deamido-NAD(+) + hydrogencarbonate = AMP + 2 H(+) +
CC pyridinium-3,5-dicarboxylate mononucleotide; Xref=Rhea:RHEA:54756,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:17544, ChEBI:CHEBI:58437,
CC ChEBI:CHEBI:137353, ChEBI:CHEBI:456215; EC=2.5.1.143;
CC Evidence={ECO:0000269|PubMed:27114550};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:27114550};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13 uM for nicotinic acid adenine dinucleotide
CC {ECO:0000269|PubMed:27114550};
CC KM=33 mM for NaHCO(3) {ECO:0000269|PubMed:27114550};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255}; Multi-pass membrane
CC protein {ECO:0000255}.
CC -!- INDUCTION: Induced by L-lactate and repressed by D-lactate. Is thus
CC regulated by the L-lactate/D-lactate ratio. Makes part of the lar
CC operon (larABCDE). {ECO:0000269|PubMed:16166538,
CC ECO:0000269|PubMed:24710389}.
CC -!- DISRUPTION PHENOTYPE: Deletion of this gene leads to a loss of lactate
CC racemase activity. {ECO:0000269|PubMed:24710389}.
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DR EMBL; AL935263; CCC77661.1; -; Genomic_DNA.
DR RefSeq; WP_011100884.1; NC_004567.2.
DR RefSeq; YP_004888175.1; NC_004567.2.
DR PDB; 7MJ0; X-ray; 3.01 A; A/B/C/D/E/F=1-246.
DR PDB; 7MJ1; X-ray; 3.40 A; A/B/C/D/E/F=1-246.
DR PDB; 7MJ2; X-ray; 2.80 A; A/B/C/D/E/F=1-246.
DR PDBsum; 7MJ0; -.
DR PDBsum; 7MJ1; -.
DR PDBsum; 7MJ2; -.
DR AlphaFoldDB; F9UST0; -.
DR SMR; F9UST0; -.
DR STRING; 220668.lp_0105; -.
DR EnsemblBacteria; CCC77661; CCC77661; lp_0105.
DR KEGG; lpl:lp_0105; -.
DR PATRIC; fig|220668.9.peg.85; -.
DR eggNOG; COG1691; Bacteria.
DR HOGENOM; CLU_065705_0_0_9; -.
DR OMA; EVIWGPG; -.
DR PhylomeDB; F9UST0; -.
DR BioCyc; LPLA220668:G1GW0-83-MON; -.
DR BioCyc; MetaCyc:MON-20305; -.
DR BRENDA; 2.5.1.143; 2849.
DR Proteomes; UP000000432; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016787; F:hydrolase activity; IEA:InterPro.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0006189; P:'de novo' IMP biosynthetic process; IEA:InterPro.
DR InterPro; IPR039476; P2CMN_synthase_LarB.
DR InterPro; IPR000031; PurE_dom.
DR PANTHER; PTHR43064; PTHR43064; 1.
DR Pfam; PF00731; AIRC; 1.
DR SMART; SM01001; AIRC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Magnesium; Membrane; Reference proteome;
KW Transferase; Transmembrane; Transmembrane helix.
FT CHAIN 1..246
FT /note="Pyridinium-3,5-biscarboxylic acid mononucleotide
FT synthase"
FT /id="PRO_0000441653"
FT TRANSMEM 172..192
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 206..228
FT /note="Helical"
FT /evidence="ECO:0000255"
FT STRAND 41..44
FT /evidence="ECO:0007829|PDB:7MJ1"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 59..69
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 83..89
FT /evidence="ECO:0007829|PDB:7MJ2"
FT TURN 90..92
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:7MJ2"
FT TURN 100..103
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 129..141
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 154..157
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 158..162
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 164..168
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 170..177
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 182..190
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 195..199
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 205..210
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 211..218
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 219..223
FT /evidence="ECO:0007829|PDB:7MJ2"
FT STRAND 225..227
FT /evidence="ECO:0007829|PDB:7MJ2"
FT HELIX 233..244
FT /evidence="ECO:0007829|PDB:7MJ2"
SQ SEQUENCE 246 AA; 25293 MW; E6B7E216FCA49C73 CRC64;
MATTAEILQQ VAAGQLSPTA AAQQLEAGKT AALGFANVDL DRQRRNGFPE VIYGAGKTAT
QIVGIVQALS QQTLPILTTR LSAEKFAALQ PALPTAVYHA TAQCMTVGEQ PAPKTPGYIA
VVTAGTSDQP VAEEAAVTAE TFGNRVERVY DVGVAGIHRL FAKLDVIRGA RVVIVIAGME
GALASVVGGL VDKPVIAVPT SVGYGTSFQG MTALLTMLNS CASGITVVNI DNGFGAAYSA
SMVNQM
