SNZ1_YEAST
ID SNZ1_YEAST Reviewed; 297 AA.
AC Q03148; D6VZR9;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit SNZ1;
DE Short=PLP synthase subunit SNZ1;
DE EC=4.3.3.6 {ECO:0000269|PubMed:19523954, ECO:0000269|PubMed:20919991};
DE AltName: Full=PDX1 homolog 1;
DE Short=Pdx1.1;
DE AltName: Full=p35;
GN Name=SNZ1; OrderedLocusNames=YMR096W; ORFNames=YM6543.03;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
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 [3]
RP PROTEIN SEQUENCE OF 1-10.
RX PubMed=14764090; DOI=10.1111/j.1432-1033.2003.03973.x;
RA Dong Y.X., Sueda S., Nikawa J., Kondo H.;
RT "Characterization of the products of the genes SNO1 and SNZ1 involved in
RT pyridoxine synthesis in Saccharomyces cerevisiae.";
RL Eur. J. Biochem. 271:745-752(2004).
RN [4]
RP IDENTIFICATION.
RX PubMed=8955308; DOI=10.1128/jb.178.23.6865-6872.1996;
RA Braun E.L., Fuge E.K., Padilla P.A., Werner-Washburne M.;
RT "A stationary-phase gene in Saccharomyces cerevisiae is a member of a
RT novel, highly conserved gene family.";
RL J. Bacteriol. 178:6865-6872(1996).
RN [5]
RP INDUCTION.
RX PubMed=9791124; DOI=10.1128/jb.180.21.5718-5726.1998;
RA Padilla P.A., Fuge E.K., Crawford M.E., Errett A., Werner-Washburne M.;
RT "The highly conserved, coregulated SNO and SNZ gene families in
RT Saccharomyces cerevisiae respond to nutrient limitation.";
RL J. Bacteriol. 180:5718-5726(1998).
RN [6]
RP ERRATUM OF PUBMED:9791124.
RA Padilla P.A., Fuge E.K., Crawford M.E., Errett A., Werner-Washburne M.;
RL J. Bacteriol. 180:6794-6794(1998).
RN [7]
RP FUNCTION, INTERACTION WITH FMP22, AND DISRUPTION PHENOTYPE.
RX PubMed=12271461; DOI=10.1002/yea.916;
RA Rodriguez-Navarro S., Llorente B., Rodriguez-Manzaneque M.T., Ramne A.,
RA Uber G., Marchesan D., Dujon B., Herrero E., Sunnerhagen P.,
RA Perez-Ortin J.E.;
RT "Functional analysis of yeast gene families involved in metabolism of
RT vitamins B1 and B6.";
RL Yeast 19:1261-1276(2002).
RN [8]
RP FUNCTION.
RX PubMed=12649274; DOI=10.1074/jbc.m300949200;
RA Stolz J., Vielreicher M.;
RT "Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces
RT cerevisiae.";
RL J. Biol. Chem. 278:18990-18996(2003).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (3.02 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=19523954; DOI=10.1016/j.febslet.2009.06.009;
RA Neuwirth M., Strohmeier M., Windeisen V., Wallner S., Deller S., Rippe K.,
RA Sinning I., Macheroux P., Tews I.;
RT "X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights
RT into the oligomeric nature of PLP synthases.";
RL FEBS Lett. 583:2179-2186(2009).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 15-297 OF APOENZYME AND IN
RP COMPLEXES WITH PYRIDOXAL PHOSPHATE AND GLYCERALDEHYDE 3-PHOSPHATE,
RP CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-116; LYS-117; 136-ARG-ARG-137;
RP LYS-148; ARG-164 AND LYS-240, AND REACTION MECHANISM.
RX PubMed=20919991; DOI=10.1042/bj20101241;
RA Zhang X., Teng Y.B., Liu J.P., He Y.X., Zhou K., Chen Y., Zhou C.Z.;
RT "Structural insights into the catalytic mechanism of the yeast pyridoxal 5-
RT phosphate synthase Snz1.";
RL Biochem. J. 432:445-450(2010).
CC -!- FUNCTION: Catalyzes the formation of pyridoxal 5'-phosphate from ribose
CC 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The
CC ammonia is provided by a SNO isoform. Can also use ribulose 5-phosphate
CC and dihydroxyacetone phosphate as substrates, resulting from enzyme-
CC catalyzed isomerization of RBP and G3P, respectively.
CC {ECO:0000269|PubMed:12271461, ECO:0000269|PubMed:12649274,
CC ECO:0000269|PubMed:19523954}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate +
CC L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-
CC phosphate; Xref=Rhea:RHEA:31507, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58273, ChEBI:CHEBI:58359, ChEBI:CHEBI:59776,
CC ChEBI:CHEBI:597326; EC=4.3.3.6;
CC Evidence={ECO:0000269|PubMed:19523954, ECO:0000269|PubMed:20919991};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.11 mM for ribose 5-phosphate {ECO:0000269|PubMed:19523954};
CC KM=0.3 mM for glyceraldehyde 3-phosphate
CC {ECO:0000269|PubMed:19523954};
CC Vmax=1.45 nmol/min/mg enzyme with ribose 5-phosphate as substrate
CC {ECO:0000269|PubMed:19523954};
CC Vmax=1.54 nmol/min/mg enzyme with glyceraldehyde 3-phosphate as
CC substrate {ECO:0000269|PubMed:19523954};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC -!- SUBUNIT: Homohexamer (PubMed:19523954). Interacts with AIM18
CC (PubMed:12271461). {ECO:0000269|PubMed:12271461,
CC ECO:0000269|PubMed:19523954}.
CC -!- INTERACTION:
CC Q03148; Q03144: SNO1; NbExp=4; IntAct=EBI-17618, EBI-28190;
CC -!- DEVELOPMENTAL STAGE: Shows increased synthesis after entry into
CC stationary phase.
CC -!- DISRUPTION PHENOTYPE: Defects cause some sensibility to 6-azauracil, an
CC inhibitor of purine and pyrimidine biosynthetic enzymes, and methylene
CC blue, a producer of singlet oxygen. These effects are probably due to
CC the inability to synthesize pyridoxal 5'-phosphate.
CC {ECO:0000269|PubMed:12271461}.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR EMBL; Z49807; CAA89897.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA09993.1; -; Genomic_DNA.
DR PIR; S55082; S55082.
DR RefSeq; NP_013814.1; NM_001182596.1.
DR PDB; 3FEM; X-ray; 3.02 A; A/B/C/D/E/F=1-297.
DR PDB; 3O05; X-ray; 2.20 A; A/B/C=15-297.
DR PDB; 3O06; X-ray; 2.35 A; A/B/C=15-297.
DR PDB; 3O07; X-ray; 1.80 A; A/B/C=15-297.
DR PDBsum; 3FEM; -.
DR PDBsum; 3O05; -.
DR PDBsum; 3O06; -.
DR PDBsum; 3O07; -.
DR AlphaFoldDB; Q03148; -.
DR SMR; Q03148; -.
DR BioGRID; 35271; 107.
DR ComplexPortal; CPX-1370; SNO1-SNZ1 pyridoxal 5'-phosphate synthase complex.
DR ComplexPortal; CPX-1371; SNO2-SNZ1 pyridoxal 5'-phosphate synthase complex.
DR DIP; DIP-1643N; -.
DR IntAct; Q03148; 9.
DR MINT; Q03148; -.
DR STRING; 4932.YMR096W; -.
DR iPTMnet; Q03148; -.
DR UCD-2DPAGE; Q03148; -.
DR MaxQB; Q03148; -.
DR PaxDb; Q03148; -.
DR PRIDE; Q03148; -.
DR EnsemblFungi; YMR096W_mRNA; YMR096W; YMR096W.
DR GeneID; 855121; -.
DR KEGG; sce:YMR096W; -.
DR SGD; S000004702; SNZ1.
DR VEuPathDB; FungiDB:YMR096W; -.
DR eggNOG; KOG1606; Eukaryota.
DR GeneTree; ENSGT00390000018460; -.
DR HOGENOM; CLU_055352_1_0_1; -.
DR InParanoid; Q03148; -.
DR OMA; EEFHINK; -.
DR BioCyc; MetaCyc:G3O-32796-MON; -.
DR BioCyc; YEAST:G3O-32796-MON; -.
DR BRENDA; 4.3.3.6; 984.
DR SABIO-RK; Q03148; -.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; Q03148; -.
DR PRO; PR:Q03148; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q03148; protein.
DR GO; GO:1903600; C:glutaminase complex; IPI:SGD.
DR GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IDA:SGD.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR GO; GO:0006543; P:glutamine catabolic process; IDA:ComplexPortal.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IDA:ComplexPortal.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:SGD.
DR GO; GO:0042819; P:vitamin B6 biosynthetic process; IMP:SGD.
DR CDD; cd04727; pdxS; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01824; PdxS; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001852; PdxS/SNZ.
DR InterPro; IPR033755; PdxS/SNZ_N.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR31829; PTHR31829; 1.
DR Pfam; PF01680; SOR_SNZ; 1.
DR PIRSF; PIRSF029271; Pdx1; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR00343; TIGR00343; 1.
DR PROSITE; PS01235; PDXS_SNZ_1; 1.
DR PROSITE; PS51129; PDXS_SNZ_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Pyridoxal phosphate;
KW Reference proteome; Schiff base.
FT CHAIN 1..297
FT /note="Pyridoxal 5'-phosphate synthase subunit SNZ1"
FT /id="PRO_0000109358"
FT ACT_SITE 80
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 23
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 152
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 164
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000269|PubMed:20919991"
FT BINDING 214
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 235..236
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT MUTAGEN 116
FT /note="E->A: No effect."
FT /evidence="ECO:0000269|PubMed:20919991"
FT MUTAGEN 117
FT /note="K->A: No activity."
FT /evidence="ECO:0000269|PubMed:20919991"
FT MUTAGEN 136..137
FT /note="RR->AA: No pyridoxal 5'-phosphate synthesis
FT activity. Retains ability to isomerize dihydroxyacetone
FT phosphate to glyceraldehyde 3-phosphate."
FT /evidence="ECO:0000269|PubMed:20919991"
FT MUTAGEN 148
FT /note="K->A: No activity."
FT /evidence="ECO:0000269|PubMed:20919991"
FT MUTAGEN 164
FT /note="R->A: No pyridoxal 5'-phosphate synthesis activity.
FT Retains ability to isomerize dihydroxyacetone phosphate to
FT glyceraldehyde 3-phosphate."
FT /evidence="ECO:0000269|PubMed:20919991"
FT MUTAGEN 240
FT /note="K->A: No effect."
FT /evidence="ECO:0000269|PubMed:20919991"
FT HELIX 4..14
FT /evidence="ECO:0007829|PDB:3FEM"
FT TURN 15..18
FT /evidence="ECO:0007829|PDB:3FEM"
FT STRAND 20..26
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 27..36
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 48..52
FT /evidence="ECO:0007829|PDB:3O07"
FT TURN 53..55
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 63..70
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 77..82
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 86..94
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 131..140
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 143..147
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:3O06"
FT HELIX 157..174
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 179..189
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 193..202
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 209..211
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 218..226
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 232..234
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 236..240
FT /evidence="ECO:0007829|PDB:3O07"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:3FEM"
FT HELIX 244..256
FT /evidence="ECO:0007829|PDB:3O07"
FT TURN 257..259
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 261..268
FT /evidence="ECO:0007829|PDB:3O07"
FT HELIX 280..282
FT /evidence="ECO:0007829|PDB:3FEM"
SQ SEQUENCE 297 AA; 31817 MW; C5BC77711B415D9F CRC64;
MTGEDFKIKS GLAQMLKGGV IMDVVTPEQA KIAEKSGACA VMALESIPAD MRKSGKVCRM
SDPKMIKDIM NSVSIPVMAK VRIGHFVEAQ IIEALEVDYI DESEVLTPAD WTHHIEKDKF
KVPFVCGAKD LGEALRRINE GAAMIRTKGE AGTGDVSEAV KHIRRITEEI KACQQLKSED
DIAKVAEEMR VPVSLLKDVL EKGKLPVVNF AAGGVATPAD AALLMQLGCD GVFVGSGIFK
SSNPVRLATA VVEATTHFDN PSKLLEVSSD LGELMGGVSI ESISHASNGV RLSEIGW
