PLPHP_YEAST
ID PLPHP_YEAST Reviewed; 257 AA.
AC P38197; D6VPW3; Q6B256;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Pyridoxal phosphate homeostasis protein {ECO:0000255|HAMAP-Rule:MF_03225};
DE Short=PLP homeostasis protein {ECO:0000255|HAMAP-Rule:MF_03225};
GN OrderedLocusNames=YBL036C; ORFNames=YBL0413;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7871888; DOI=10.1002/yea.320101113;
RA de Wergifosse P., Jacques B., Jonniaux J.-L., Purnelle B., Skala J.,
RA Goffeau A.;
RT "The sequence of a 22.4 kb DNA fragment from the left arm of yeast
RT chromosome II reveals homologues to bacterial proline synthetase and murine
RT alpha-adaptin, as well as a new permease and a DNA-binding protein.";
RL Yeast 10:1489-1496(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA Mewes H.-W., Kleine K.;
RT "Complete DNA sequence of yeast chromosome II.";
RL EMBO J. 13:5795-5809(1994).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), AND PYRIDOXAL PHOSPHATE AT LYS-49.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=12499548; DOI=10.1107/s0907444902018012;
RA Eswaramoorthy S., Gerchman S., Graziano V., Kycia H., Studier W.,
RA Swaminathan S.;
RT "Structure of a yeast hypothetical protein selected by a structural
RT genomics approach.";
RL Acta Crystallogr. D 59:127-135(2003).
CC -!- FUNCTION: Pyridoxal 5'-phosphate (PLP)-binding protein, which may be
CC involved in intracellular homeostatic regulation of pyridoxal 5'-
CC phosphate (PLP), the active form of vitamin B6. {ECO:0000255|HAMAP-
CC Rule:MF_03225}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 4890 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the pyridoxal phosphate-binding protein
CC YggS/PROSC family. {ECO:0000255|HAMAP-Rule:MF_03225}.
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DR EMBL; X78214; CAA55058.1; -; Genomic_DNA.
DR EMBL; Z35797; CAA84856.1; -; Genomic_DNA.
DR EMBL; AY692874; AAT92893.1; -; Genomic_DNA.
DR EMBL; BK006936; DAA07083.1; -; Genomic_DNA.
DR PIR; S50294; S50294.
DR RefSeq; NP_009517.1; NM_001178276.1.
DR PDB; 1B54; X-ray; 2.10 A; A=1-257.
DR PDB; 1CT5; X-ray; 2.00 A; A=2-257.
DR PDBsum; 1B54; -.
DR PDBsum; 1CT5; -.
DR AlphaFoldDB; P38197; -.
DR SMR; P38197; -.
DR BioGRID; 32661; 93.
DR DIP; DIP-6608N; -.
DR IntAct; P38197; 17.
DR MINT; P38197; -.
DR STRING; 4932.YBL036C; -.
DR iPTMnet; P38197; -.
DR MaxQB; P38197; -.
DR PaxDb; P38197; -.
DR PRIDE; P38197; -.
DR EnsemblFungi; YBL036C_mRNA; YBL036C; YBL036C.
DR GeneID; 852244; -.
DR KEGG; sce:YBL036C; -.
DR SGD; S000000132; YBL036C.
DR VEuPathDB; FungiDB:YBL036C; -.
DR eggNOG; KOG3157; Eukaryota.
DR GeneTree; ENSGT00390000004928; -.
DR HOGENOM; CLU_059988_2_0_1; -.
DR InParanoid; P38197; -.
DR OMA; IEWHMIG; -.
DR BioCyc; YEAST:G3O-28938-MON; -.
DR EvolutionaryTrace; P38197; -.
DR PRO; PR:P38197; -.
DR Proteomes; UP000002311; Chromosome II.
DR RNAct; P38197; protein.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:SGD.
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; Acetylation; Cytoplasm; Nucleus; Pyridoxal phosphate;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..257
FT /note="Pyridoxal phosphate homeostasis protein"
FT /id="PRO_0000163213"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 49
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03225,
FT ECO:0000269|PubMed:12499548"
FT CONFLICT 8
FT /note="D -> G (in Ref. 4; AAT92893)"
FT /evidence="ECO:0000305"
FT HELIX 9..31
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 72..81
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 87..90
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 99..104
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 108..114
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 117..130
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:1B54"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 157..168
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 174..181
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 197..213
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:1CT5"
FT TURN 224..226
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 227..232
FT /evidence="ECO:0007829|PDB:1CT5"
FT STRAND 236..241
FT /evidence="ECO:0007829|PDB:1CT5"
FT HELIX 242..245
FT /evidence="ECO:0007829|PDB:1CT5"
SQ SEQUENCE 257 AA; 29123 MW; 5643EE0D36B6D85A CRC64;
MSTGITYDED RKTQLIAQYE SVREVVNAEA KNVHVNENAS KILLLVVSKL KPASDIQILY
DHGVREFGEN YVQELIEKAK LLPDDIKWHF IGGLQTNKCK DLAKVPNLYS VETIDSLKKA
KKLNESRAKF QPDCNPILCN VQINTSHEDQ KSGLNNEAEI FEVIDFFLSE ECKYIKLNGL
MTIGSWNVSH EDSKENRDFA TLVEWKKKID AKFGTSLKLS MGMSADFREA IRQGTAEVRI
GTDIFGARPP KNEARII
