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Lactate racemase (Lar) (EC 5.1.2.1) (Lactate racemization operon protein LarA)

 LARA_LACPL              Reviewed;         424 AA.
F9USS9;
27-SEP-2017, integrated into UniProtKB/Swiss-Prot.
19-OCT-2011, sequence version 1.
05-DEC-2018, entry version 43.
RecName: Full=Lactate racemase {ECO:0000303|PubMed:24710389};
Short=Lar {ECO:0000303|PubMed:24710389};
EC=5.1.2.1 {ECO:0000269|PubMed:24710389, ECO:0000269|PubMed:26138974};
AltName: Full=Lactate racemization operon protein LarA {ECO:0000303|PubMed:16166538, ECO:0000312|EMBL:CCC77660.1};
Name=larA {ECO:0000303|PubMed:16166538, ECO:0000312|EMBL:CCC77660.1};
OrderedLocusNames=lp_0104 {ECO:0000312|EMBL:CCC77660.1};
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1).
Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
Lactobacillus.
NCBI_TaxID=220668;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
PubMed=12566566; DOI=10.1073/pnas.0337704100;
Kleerebezem M., Boekhorst J., van Kranenburg R., Molenaar D.,
Kuipers O.P., Leer R., Tarchini R., Peters S.A., Sandbrink H.M.,
Fiers M.W.E.J., Stiekema W., Klein Lankhorst R.M., Bron P.A.,
Hoffer S.M., Nierop Groot M.N., Kerkhoven R., De Vries M., Ursing B.,
De Vos W.M., Siezen R.J.;
"Complete genome sequence of Lactobacillus plantarum WCFS1.";
Proc. Natl. Acad. Sci. U.S.A. 100:1990-1995(2003).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND GENOME
REANNOTATION.
STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
PubMed=22156394; DOI=10.1128/JB.06275-11;
Siezen R.J., Francke C., Renckens B., Boekhorst J., Wels M.,
Kleerebezem M., van Hijum S.A.;
"Complete resequencing and reannotation of the Lactobacillus plantarum
WCFS1 genome.";
J. Bacteriol. 194:195-196(2012).
[3]
FUNCTION, AND INDUCTION.
STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
PubMed=16166538; DOI=10.1128/JB.187.19.6750-6761.2005;
Goffin P., Deghorain M., Mainardi J.L., Tytgat I.,
Champomier-Verges M.C., Kleerebezem M., Hols P.;
"Lactate racemization as a rescue pathway for supplying D-lactate to
the cell wall biosynthesis machinery in Lactobacillus plantarum.";
J. Bacteriol. 187:6750-6761(2005).
[4]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
ACTIVITY REGULATION, INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
PubMed=24710389; DOI=10.1038/NCOMMS4615;
Desguin B., Goffin P., Viaene E., Kleerebezem M.,
Martin-Diaconescu V., Maroney M.J., Declercq J.P., Soumillion P.,
Hols P.;
"Lactate racemase is a nickel-dependent enzyme activated by a
widespread maturation system.";
Nat. Commun. 5:3615-3615(2014).
[5]
INDUCTION.
STRAIN=ATCC BAA-793 / NCIMB 8826 / WCFS1;
PubMed=25349156; DOI=10.1128/JB.02192-14;
Desguin B., Goffin P., Bakouche N., Diman A., Viaene E., Dandoy D.,
Fontaine L., Hallet B., Hols P.;
"Enantioselective regulation of lactate racemization by LarR in
Lactobacillus plantarum.";
J. Bacteriol. 197:219-230(2015).
[6]
ACTIVITY REGULATION, AND COFACTOR.
PubMed=27114550; DOI=10.1073/pnas.1600486113;
Desguin B., Soumillion P., Hols P., Hausinger R.P.;
"Nickel-pincer cofactor biosynthesis involves LarB-catalyzed
pyridinium carboxylation and LarE-dependent sacrificial sulfur
insertion.";
Proc. Natl. Acad. Sci. U.S.A. 113:5598-5603(2016).
[7]
X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) OF 2-424 IN COMPLEX WITH
(SCS)NI COFACTOR, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY
REGULATION, MUTAGENESIS OF ASP-72; ARG-75; HIS-108; HIS-174; LYS-184;
HIS-200; GLN-295 AND LYS-298, REACTION MECHANISM, AND ACTIVE SITE.
PubMed=26138974; DOI=10.1126/science.aab2272;
Desguin B., Zhang T., Soumillion P., Hols P., Hu J., Hausinger R.P.;
"METALLOPROTEINS. A tethered niacin-derived pincer complex with a
nickel-carbon bond in lactate racemase.";
Science 349:66-69(2015).
-!- FUNCTION: Catalyzes the interconversion between the D- and L-
isomers of lactate (PubMed:24710389, PubMed:26138974). May act as
a rescue enzyme to ensure D-lactate production in physiological
conditions where its production by the D-lactate dehydrogenase
LdhD is not sufficient (PubMed:16166538). D-Lactate is absolutely
required for growth of L.plantarum and is an essential component
of the cell wall peptidoglycan in this species, where it is
incorporated as the last residue of the muramoyl-pentadepsipeptide
peptidoglycan precursor; its incorporation confers high level of
vancomycin resistance (PubMed:16166538).
{ECO:0000269|PubMed:16166538, ECO:0000269|PubMed:24710389,
ECO:0000269|PubMed:26138974}.
-!- CATALYTIC ACTIVITY:
Reaction=(S)-lactate = (R)-lactate; Xref=Rhea:RHEA:10960,
ChEBI:CHEBI:16004, ChEBI:CHEBI:16651; EC=5.1.2.1;
Evidence={ECO:0000269|PubMed:24710389,
ECO:0000269|PubMed:26138974};
-!- COFACTOR:
Name=Ni(II)-pyridinium-3,5-bisthiocarboxylate mononucleotide;
Xref=ChEBI:CHEBI:137373; Evidence={ECO:0000269|PubMed:26138974};
Note=Was originally shown to use Ni(2+) as a cofactor
(PubMed:24710389), but in fact, the cofactor is a (SCS)Ni pincer
complex, a nicotinic acid mononucleotide derivative that is
covalently attached to Lys-184 and forms a tridentate pincer
complex that coordinates nickel through one metal-carbon and two
metal-sulfur bonds (PubMed:26138974, PubMed:27114550).
{ECO:0000269|PubMed:24710389, ECO:0000269|PubMed:26138974,
ECO:0000269|PubMed:27114550};
-!- ACTIVITY REGULATION: Activation of the apo-enzyme requires the
three accessory proteins LarB, LarE and LarC, that are involved in
the biosynthesis of the nickel-pincer cofactor of LarA
(PubMed:24710389, PubMed:27114550). Inhibited by sulfite that
behaves as a mixed inhibitor (PubMed:26138974).
{ECO:0000269|PubMed:24710389, ECO:0000269|PubMed:26138974,
ECO:0000269|PubMed:27114550}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=46 mM for L-lactate {ECO:0000269|PubMed:24710389};
KM=11 mM for D-lactate {ECO:0000269|PubMed:24710389};
Note=kcat is 4745 sec(-1) for conversion of L-lactate to D-
lactate. kcat is 1333 sec(-1) for conversion of D-lactate to L-
lactate. {ECO:0000269|PubMed:24710389};
-!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:D9TQ02}.
-!- INDUCTION: Induced by L-lactate and repressed by D-lactate. The
lactate racemase activity is thus regulated by the L-lactate/D-
lactate ratio, under the control of the transcriptional regulator
LarR. Makes part of the lar operon (larABCDE).
{ECO:0000269|PubMed:16166538, ECO:0000269|PubMed:24710389,
ECO:0000269|PubMed:25349156}.
-!- DISRUPTION PHENOTYPE: Deletion of this gene leads to a loss of
lactate racemase activity. {ECO:0000269|PubMed:24710389}.
-!- SIMILARITY: Belongs to the lactate racemase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL935263; CCC77660.1; -; Genomic_DNA.
RefSeq; WP_011100883.1; NC_004567.2.
RefSeq; YP_004888174.1; NC_004567.2.
PDB; 5HUQ; X-ray; 3.00 A; A/B=2-424.
PDB; 6C1W; X-ray; 2.40 A; A/B/C=1-424.
PDBsum; 5HUQ; -.
PDBsum; 6C1W; -.
SMR; F9USS9; -.
STRING; 220668.lp_0104; -.
DNASU; 1061369; -.
EnsemblBacteria; CCC77660; CCC77660; lp_0104.
GeneID; 1061369; -.
KEGG; lpl:lp_0104; -.
PATRIC; fig|220668.9.peg.84; -.
eggNOG; ENOG4105QUH; Bacteria.
eggNOG; COG3875; LUCA.
KO; K22373; -.
OMA; GSVEPHY; -.
BioCyc; LPLA220668:G1GW0-82-MONOMER; -.
BioCyc; MetaCyc:MONOMER-19498; -.
Proteomes; UP000000432; Chromosome.
GO; GO:0050043; F:lactate racemase activity; IEA:UniProtKB-EC.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
InterPro; IPR018657; LarA-like_N.
Pfam; PF09861; Lar_N; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Isomerase; Metal-binding; Nickel;
Reference proteome.
CHAIN 1 424 Lactate racemase.
/FTId=PRO_0000441651.
REGION 72 75 Cofactor binding.
{ECO:0000269|PubMed:26138974}.
ACT_SITE 108 108 Proton donor/acceptor.
{ECO:0000305|PubMed:26138974}.
ACT_SITE 174 174 Proton donor/acceptor.
{ECO:0000305|PubMed:26138974}.
METAL 200 200 Nickel. {ECO:0000269|PubMed:26138974}.
BINDING 184 184 Cofactor (covalent).
{ECO:0000269|PubMed:26138974,
ECO:0000269|PubMed:27114550}.
BINDING 295 295 Substrate. {ECO:0000305|PubMed:26138974}.
BINDING 298 298 Substrate. {ECO:0000305|PubMed:26138974}.
MUTAGEN 72 72 D->A: Shows residual catalytic activity
in vivo. {ECO:0000269|PubMed:26138974}.
MUTAGEN 75 75 R->A: Retains some catalytic activity in
vitro. Exhibits reduced Ni content.
{ECO:0000269|PubMed:26138974}.
MUTAGEN 108 108 H->A: Loss of catalytic activity.
{ECO:0000269|PubMed:26138974}.
MUTAGEN 174 174 H->A: Loss of catalytic activity.
Exhibits reduced Ni content.
{ECO:0000269|PubMed:26138974}.
MUTAGEN 184 184 K->A: Shows residual catalytic activity
in vivo. Loss of Ni binding.
{ECO:0000269|PubMed:26138974}.
MUTAGEN 200 200 H->A: Loss of catalytic activity.
{ECO:0000269|PubMed:26138974}.
MUTAGEN 295 295 Q->A: Retains some catalytic activity in
vitro. Exhibits reduced Ni content.
{ECO:0000269|PubMed:26138974}.
MUTAGEN 298 298 K->A: Loss of catalytic activity.
{ECO:0000269|PubMed:26138974}.
STRAND 2 8 {ECO:0000244|PDB:6C1W}.
STRAND 11 17 {ECO:0000244|PDB:6C1W}.
TURN 19 21 {ECO:0000244|PDB:6C1W}.
STRAND 22 25 {ECO:0000244|PDB:6C1W}.
TURN 29 32 {ECO:0000244|PDB:6C1W}.
HELIX 39 48 {ECO:0000244|PDB:6C1W}.
STRAND 51 53 {ECO:0000244|PDB:6C1W}.
HELIX 56 59 {ECO:0000244|PDB:6C1W}.
TURN 60 62 {ECO:0000244|PDB:6C1W}.
STRAND 64 71 {ECO:0000244|PDB:6C1W}.
HELIX 79 93 {ECO:0000244|PDB:6C1W}.
STRAND 97 104 {ECO:0000244|PDB:6C1W}.
HELIX 113 120 {ECO:0000244|PDB:6C1W}.
HELIX 122 127 {ECO:0000244|PDB:6C1W}.
STRAND 128 132 {ECO:0000244|PDB:6C1W}.
HELIX 138 140 {ECO:0000244|PDB:6C1W}.
STRAND 141 146 {ECO:0000244|PDB:6C1W}.
STRAND 150 156 {ECO:0000244|PDB:6C1W}.
HELIX 157 160 {ECO:0000244|PDB:6C1W}.
STRAND 163 170 {ECO:0000244|PDB:6C1W}.
TURN 175 177 {ECO:0000244|PDB:6C1W}.
STRAND 178 181 {ECO:0000244|PDB:5HUQ}.
HELIX 182 185 {ECO:0000244|PDB:6C1W}.
TURN 186 190 {ECO:0000244|PDB:6C1W}.
HELIX 193 199 {ECO:0000244|PDB:6C1W}.
HELIX 202 205 {ECO:0000244|PDB:6C1W}.
HELIX 219 230 {ECO:0000244|PDB:6C1W}.
STRAND 233 241 {ECO:0000244|PDB:6C1W}.
STRAND 247 254 {ECO:0000244|PDB:6C1W}.
HELIX 257 270 {ECO:0000244|PDB:6C1W}.
STRAND 271 273 {ECO:0000244|PDB:6C1W}.
STRAND 277 283 {ECO:0000244|PDB:6C1W}.
STRAND 289 292 {ECO:0000244|PDB:6C1W}.
HELIX 293 306 {ECO:0000244|PDB:6C1W}.
STRAND 307 316 {ECO:0000244|PDB:6C1W}.
HELIX 326 333 {ECO:0000244|PDB:6C1W}.
HELIX 338 347 {ECO:0000244|PDB:6C1W}.
HELIX 350 352 {ECO:0000244|PDB:6C1W}.
HELIX 357 369 {ECO:0000244|PDB:6C1W}.
STRAND 370 375 {ECO:0000244|PDB:6C1W}.
STRAND 377 379 {ECO:0000244|PDB:6C1W}.
HELIX 381 386 {ECO:0000244|PDB:6C1W}.
STRAND 390 394 {ECO:0000244|PDB:6C1W}.
HELIX 395 406 {ECO:0000244|PDB:6C1W}.
STRAND 412 414 {ECO:0000244|PDB:6C1W}.
STRAND 418 420 {ECO:0000244|PDB:6C1W}.
STRAND 422 424 {ECO:0000244|PDB:6C1W}.
SEQUENCE 424 AA; 46239 MW; 063CD5E0D19710D5 CRC64;
MVAIDLPYDK RTITAQIDDE NYAGKLVSQA ATYHNKLSEQ ETVEKSLDNP IGSDKLEELA
RGKHNIVIIS SDHTRPVPSH IITPILLRRL RSVAPDARIR ILVATGFHRP STHEELVNKY
GEDIVNNEEI VMHVSTDDSS MVKIGQLPSG GDCIINKVAA EADLLISEGF IESHFFAGFS
GGRKSVLPGI ASYKTIMANH SGEFINSPKA RTGNLMHNSI HKDMVYAART AKLAFIINVV
LDEDKKIIGS FAGDMEAAHK VGCDFVKELS SVPAIDCDIA ISTNGGYPLD QNIYQAVKGM
TAAEATNKEG GTIIMVAGAR DGHGGEGFYH NLADVDDPKE FLDQAINTPR LKTIPDQWTA
QIFARILVHH HVIFVSDLVD PDLITNMHME LAKTLDEAME KAYAREGQAA KVTVIPDGLG
VIVK


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