PLPHP_ECOLI
ID PLPHP_ECOLI Reviewed; 234 AA.
AC P67080; P52054; Q2M9P2;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Pyridoxal phosphate homeostasis protein {ECO:0000255|HAMAP-Rule:MF_02087, ECO:0000305};
DE Short=PLP homeostasis protein {ECO:0000255|HAMAP-Rule:MF_02087, ECO:0000305};
GN Name=yggS; OrderedLocusNames=b2951, JW2918;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP DISRUPTION PHENOTYPE, LACK OF RACEMASE ACTIVITY, AND MUTAGENESIS OF LYS-36.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=24097949; DOI=10.1128/jb.00593-13;
RA Ito T., Iimori J., Takayama S., Moriyama A., Yamauchi A., Hemmi H.,
RA Yoshimura T.;
RT "Conserved pyridoxal protein that regulates Ile and Val metabolism.";
RL J. Bacteriol. 195:5439-5449(2013).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=27426274; DOI=10.1016/j.jbiosc.2016.06.010;
RA Ito T., Yamauchi A., Hemmi H., Yoshimura T.;
RT "Ophthalmic acid accumulation in an Escherichia coli mutant lacking the
RT conserved pyridoxal 5'-phosphate-binding protein YggS.";
RL J. Biosci. Bioeng. 122:689-693(2016).
RN [5]
RP FUNCTION, SUBUNIT, AND DISRUPTION PHENOTYPE.
RX PubMed=26872910; DOI=10.1099/mic.0.000255;
RA Prunetti L., El Yacoubi B., Schiavon C.R., Kirkpatrick E., Huang L.,
RA Bailly M., ElBadawi-Sidhu M., Harrison K., Gregory J.F., Fiehn O.,
RA Hanson A.D., de Crecy-Lagard V.;
RT "Evidence that COG0325 proteins are involved in PLP homeostasis.";
RL Microbiology 162:694-706(2016).
RN [6] {ECO:0007744|PDB:1W8G}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE.
RA Sulzenbacher G., Gruez A., Spinelli S., Roig-Zamboni V., Pagot F.,
RA Bignon C., Vincentelli R., Cambillau C.;
RT "Crystal structure of E. coli K-12 YggS.";
RL Submitted (SEP-2004) to the PDB data bank.
RN [7] {ECO:0007744|PDB:3SY1}
RP X-RAY CRYSTALLOGRAPHY (1.47 ANGSTROMS).
RA Vorobiev S., Su M., Nivon L., Seetharaman J., Sahdev S., Xiao R.,
RA Ciccosanti C., Maglaqui M., Baker D., Everett J.K., Nair R., Acton T.B.,
RA Rost B., Montelione G.T., Hunt J.F., Tong L.;
RT "Crystal structure of engineered protein. Northeast structural genomics
RT consortium target OR70.";
RL Submitted (JUL-2011) to the PDB data bank.
CC -!- FUNCTION: Pyridoxal 5'-phosphate (PLP)-binding protein, which is
CC involved in PLP homeostasis. May have a carrier function to deliver PLP
CC to the target enzymes or a protective function so that PLP does not
CC inactivate essential lysines in proteins (PubMed:26872910). Does not
CC have amino acid racemase activity (PubMed:24097949).
CC {ECO:0000269|PubMed:24097949, ECO:0000269|PubMed:26872910}.
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_02087,
CC ECO:0000269|PubMed:26872910}.
CC -!- DISRUPTION PHENOTYPE: During the stationary phase, the deletion mutant
CC exhibits a completely different intracellular pool of amino acids and
CC produces a significant amount of L-valine in the culture medium. The
CC log-phase mutant displays slightly decreased coenzyme A levels,
CC accumulates 2-ketobutyrate, 2-aminobutyrate, and, to a lesser extent,
CC L-valine. Also exhibits an increase in the levels of isoleucine and
CC valine metabolic enzymes (PubMed:24097949). The mutant also accumulates
CC gamma-L-glutamyl-L-2-aminobutyryl-glycine (ophthalmic acid)
CC (PubMed:27426274). The mutant accumulates the PLP precursor pyridoxine
CC 5'-phosphate (PNP), and is sensitive to an excess of pyridoxine but not
CC of pyridoxal (PubMed:26872910). Most of the phenotypes observed in the
CC absence of yggS are probably caused by lower activities of PLP-
CC dependent enzymes (PubMed:26872910). {ECO:0000269|PubMed:24097949,
CC ECO:0000269|PubMed:26872910, ECO:0000269|PubMed:27426274,
CC ECO:0000305|PubMed:26872910}.
CC -!- SIMILARITY: Belongs to the pyridoxal phosphate-binding protein
CC YggS/PROSC family. {ECO:0000255|HAMAP-Rule:MF_02087, ECO:0000305}.
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DR EMBL; U28377; AAA69118.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75988.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77014.1; -; Genomic_DNA.
DR PIR; F65080; F65080.
DR RefSeq; NP_417426.1; NC_000913.3.
DR RefSeq; WP_000997795.1; NZ_STEB01000001.1.
DR PDB; 1W8G; X-ray; 2.00 A; A=1-234.
DR PDB; 3SY1; X-ray; 1.46 A; A=1-234.
DR PDBsum; 1W8G; -.
DR PDBsum; 3SY1; -.
DR AlphaFoldDB; P67080; -.
DR SMR; P67080; -.
DR BioGRID; 4261786; 34.
DR BioGRID; 851744; 1.
DR DIP; DIP-12194N; -.
DR IntAct; P67080; 9.
DR STRING; 511145.b2951; -.
DR jPOST; P67080; -.
DR PaxDb; P67080; -.
DR PRIDE; P67080; -.
DR EnsemblBacteria; AAC75988; AAC75988; b2951.
DR EnsemblBacteria; BAE77014; BAE77014; BAE77014.
DR GeneID; 66673167; -.
DR GeneID; 947423; -.
DR KEGG; ecj:JW2918; -.
DR KEGG; eco:b2951; -.
DR PATRIC; fig|1411691.4.peg.3781; -.
DR EchoBASE; EB2804; -.
DR eggNOG; COG0325; Bacteria.
DR HOGENOM; CLU_059988_0_1_6; -.
DR InParanoid; P67080; -.
DR OMA; IEWHMIG; -.
DR PhylomeDB; P67080; -.
DR BioCyc; EcoCyc:G7527-MON; -.
DR EvolutionaryTrace; P67080; -.
DR PRO; PR:P67080; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR Gene3D; 3.20.20.10; -; 1.
DR HAMAP; MF_02087; PLP_homeostasis; 1.
DR InterPro; IPR001608; Ala_racemase_N.
DR InterPro; IPR029066; PLP-binding_barrel.
DR InterPro; IPR011078; PyrdxlP_homeostasis.
DR PANTHER; PTHR10146; PTHR10146; 1.
DR Pfam; PF01168; Ala_racemase_N; 1.
DR PIRSF; PIRSF004848; YBL036c_PLPDEIII; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR00044; TIGR00044; 1.
DR PROSITE; PS01211; UPF0001; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..234
FT /note="Pyridoxal phosphate homeostasis protein"
FT /id="PRO_0000163196"
FT MOD_RES 36
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02087,
FT ECO:0000269|Ref.6, ECO:0007744|PDB:1W8G"
FT MUTAGEN 36
FT /note="K->A: Does not bind PLP."
FT /evidence="ECO:0000269|PubMed:24097949"
FT HELIX 3..21
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 40..48
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 53..58
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 59..72
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 90..96
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 106..115
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 123..129
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 145..153
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 158..164
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 173..191
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:1W8G"
FT HELIX 208..214
FT /evidence="ECO:0007829|PDB:3SY1"
FT STRAND 218..222
FT /evidence="ECO:0007829|PDB:3SY1"
FT HELIX 223..226
FT /evidence="ECO:0007829|PDB:3SY1"
SQ SEQUENCE 234 AA; 25787 MW; 2AA431E2D75BCA59 CRC64;
MNDIAHNLAQ VRDKISAAAT RCGRSPEEIT LLAVSKTKPA SAIAEAIDAG QRQFGENYVQ
EGVDKIRHFQ ELGVTGLEWH FIGPLQSNKS RLVAEHFDWC HTIDRLRIAT RLNDQRPAEL
PPLNVLIQIN ISDENSKSGI QLAELDELAA AVAELPRLRL RGLMAIPAPE SEYVRQFEVA
RQMAVAFAGL KTRYPHIDTL SLGMSDDMEA AIAAGSTMVR IGTAIFGARD YSKK
