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Protein

Pyridoxal 5'-phosphate synthase subunit SNZ1

Gene

SNZ1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by a SNO isoform. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively.3 Publications

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.2 Publications

Kineticsi

  1. KM=0.11 mM for ribose 5-phosphate1 Publication
  2. KM=0.3 mM for glyceraldehyde 3-phosphate1 Publication
  1. Vmax=1.45 nmol/min/mg enzyme with ribose 5-phosphate as substrate1 Publication
  2. Vmax=1.54 nmol/min/mg enzyme with glyceraldehyde 3-phosphate as substrate1 Publication

Pathwayi: pyridoxal 5'-phosphate biosynthesis

This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei23 – 231D-ribose 5-phosphateBy similarity
Active sitei80 – 801Schiff-base intermediate with D-ribose 5-phosphateBy similarity
Binding sitei152 – 1521D-ribose 5-phosphate; via amide nitrogenBy similarity
Binding sitei164 – 1641Glyceraldehyde 3-phosphate1 Publication
Binding sitei214 – 2141D-ribose 5-phosphate; via amide nitrogenBy similarity

GO - Molecular functioni

GO - Biological processi

  • pyridoxal phosphate biosynthetic process Source: UniProtKB-UniPathway
  • pyridoxine biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Pyridoxal phosphate, Schiff base

Enzyme and pathway databases

BioCyciMetaCyc:G3O-32796-MONOMER.
YEAST:G3O-32796-MONOMER.
BRENDAi4.3.3.6. 984.
UniPathwayiUPA00245.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal 5'-phosphate synthase subunit SNZ1 (EC:4.3.3.62 Publications)
Short name:
PLP synthase subunit SNZ1
Alternative name(s):
PDX1 homolog 1
Short name:
Pdx1.1
p35
Gene namesi
Name:SNZ1
Ordered Locus Names:YMR096W
ORF Names:YM6543.03
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR096W.
SGDiS000004702. SNZ1.

Subcellular locationi

GO - Cellular componenti

  • glutaminase complex Source: SGD
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Defects cause some sensibility to 6-azauracil, an inhibitor of purine and pyrimidine biosynthetic enzymes, and methylene blue, a producer of singlet oxygen. These effects are probably due to the inability to synthesize pyridoxal 5'-phosphate.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi116 – 1161E → A: No effect. 1 Publication
Mutagenesisi117 – 1171K → A: No activity. 1 Publication
Mutagenesisi136 – 1372RR → AA: No pyridoxal 5'-phosphate synthesis activity. Retains ability to isomerize dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. 1 Publication
Mutagenesisi148 – 1481K → A: No activity. 1 Publication
Mutagenesisi164 – 1641R → A: No pyridoxal 5'-phosphate synthesis activity. Retains ability to isomerize dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. 1 Publication
Mutagenesisi240 – 2401K → A: No effect. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 297297Pyridoxal 5'-phosphate synthase subunit SNZ1PRO_0000109358Add
BLAST

Proteomic databases

MaxQBiQ03148.
PeptideAtlasiQ03148.

2D gel databases

UCD-2DPAGEQ03148.

Expressioni

Developmental stagei

Shows increased synthesis after entry into stationary phase.

Interactioni

Subunit structurei

Homohexamer (PubMed:19523954). Interacts with AIM18 (PubMed:12271461).2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SNO1Q031444EBI-17618,EBI-28190

Protein-protein interaction databases

BioGridi35271. 40 interactions.
DIPiDIP-1643N.
IntActiQ03148. 9 interactions.
MINTiMINT-386894.

Structurei

Secondary structure

1
297
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1411Combined sources
Turni15 – 184Combined sources
Beta strandi20 – 267Combined sources
Helixi27 – 3610Combined sources
Beta strandi39 – 435Combined sources
Helixi48 – 525Combined sources
Turni53 – 553Combined sources
Helixi63 – 708Combined sources
Beta strandi77 – 826Combined sources
Helixi86 – 949Combined sources
Beta strandi98 – 1036Combined sources
Helixi117 – 1193Combined sources
Beta strandi124 – 1307Combined sources
Helixi131 – 14010Combined sources
Beta strandi143 – 1475Combined sources
Beta strandi151 – 1533Combined sources
Helixi157 – 17418Combined sources
Helixi179 – 18911Combined sources
Helixi193 – 20210Combined sources
Beta strandi209 – 2113Combined sources
Helixi218 – 2269Combined sources
Beta strandi232 – 2343Combined sources
Helixi236 – 2405Combined sources
Beta strandi241 – 2433Combined sources
Helixi244 – 25613Combined sources
Turni257 – 2593Combined sources
Helixi261 – 2688Combined sources
Helixi280 – 2823Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FEMX-ray3.02A/B/C/D/E/F1-297[»]
3O05X-ray2.20A/B/C15-297[»]
3O06X-ray2.35A/B/C15-297[»]
3O07X-ray1.80A/B/C15-297[»]
ProteinModelPortaliQ03148.
SMRiQ03148. Positions 16-274.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ03148.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni235 – 2362D-ribose 5-phosphate bindingBy similarity

Sequence similaritiesi

Belongs to the PdxS/SNZ family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000018460.
HOGENOMiHOG000227586.
InParanoidiQ03148.
KOiK06215.
OMAiVQASTHY.
OrthoDBiEOG7TN031.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF01680. SOR_SNZ. 1 hit.
[Graphical view]
PIRSFiPIRSF029271. Pdx1. 1 hit.
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q03148-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTGEDFKIKS GLAQMLKGGV IMDVVTPEQA KIAEKSGACA VMALESIPAD
60 70 80 90 100
MRKSGKVCRM SDPKMIKDIM NSVSIPVMAK VRIGHFVEAQ IIEALEVDYI
110 120 130 140 150
DESEVLTPAD WTHHIEKDKF KVPFVCGAKD LGEALRRINE GAAMIRTKGE
160 170 180 190 200
AGTGDVSEAV KHIRRITEEI KACQQLKSED DIAKVAEEMR VPVSLLKDVL
210 220 230 240 250
EKGKLPVVNF AAGGVATPAD AALLMQLGCD GVFVGSGIFK SSNPVRLATA
260 270 280 290
VVEATTHFDN PSKLLEVSSD LGELMGGVSI ESISHASNGV RLSEIGW
Length:297
Mass (Da):31,817
Last modified:November 1, 1997 - v1
Checksum:iC5BC77711B415D9F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49807 Genomic DNA. Translation: CAA89897.1.
BK006946 Genomic DNA. Translation: DAA09993.1.
PIRiS55082.
RefSeqiNP_013814.1. NM_001182596.1.

Genome annotation databases

EnsemblFungiiYMR096W; YMR096W; YMR096W.
GeneIDi855121.
KEGGisce:YMR096W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49807 Genomic DNA. Translation: CAA89897.1.
BK006946 Genomic DNA. Translation: DAA09993.1.
PIRiS55082.
RefSeqiNP_013814.1. NM_001182596.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FEMX-ray3.02A/B/C/D/E/F1-297[»]
3O05X-ray2.20A/B/C15-297[»]
3O06X-ray2.35A/B/C15-297[»]
3O07X-ray1.80A/B/C15-297[»]
ProteinModelPortaliQ03148.
SMRiQ03148. Positions 16-274.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35271. 40 interactions.
DIPiDIP-1643N.
IntActiQ03148. 9 interactions.
MINTiMINT-386894.

2D gel databases

UCD-2DPAGEQ03148.

Proteomic databases

MaxQBiQ03148.
PeptideAtlasiQ03148.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR096W; YMR096W; YMR096W.
GeneIDi855121.
KEGGisce:YMR096W.

Organism-specific databases

EuPathDBiFungiDB:YMR096W.
SGDiS000004702. SNZ1.

Phylogenomic databases

GeneTreeiENSGT00390000018460.
HOGENOMiHOG000227586.
InParanoidiQ03148.
KOiK06215.
OMAiVQASTHY.
OrthoDBiEOG7TN031.

Enzyme and pathway databases

UniPathwayiUPA00245.
BioCyciMetaCyc:G3O-32796-MONOMER.
YEAST:G3O-32796-MONOMER.
BRENDAi4.3.3.6. 984.

Miscellaneous databases

EvolutionaryTraceiQ03148.
NextBioi978476.
PROiQ03148.

Family and domain databases

Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]
PfamiPF01680. SOR_SNZ. 1 hit.
[Graphical view]
PIRSFiPIRSF029271. Pdx1. 1 hit.
SUPFAMiSSF51366. SSF51366. 1 hit.
TIGRFAMsiTIGR00343. TIGR00343. 1 hit.
PROSITEiPS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Characterization of the products of the genes SNO1 and SNZ1 involved in pyridoxine synthesis in Saccharomyces cerevisiae."
    Dong Y.X., Sueda S., Nikawa J., Kondo H.
    Eur. J. Biochem. 271:745-752(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-10.
  4. "A stationary-phase gene in Saccharomyces cerevisiae is a member of a novel, highly conserved gene family."
    Braun E.L., Fuge E.K., Padilla P.A., Werner-Washburne M.
    J. Bacteriol. 178:6865-6872(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  5. "The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation."
    Padilla P.A., Fuge E.K., Crawford M.E., Errett A., Werner-Washburne M.
    J. Bacteriol. 180:5718-5726(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  6. Erratum
    Padilla P.A., Fuge E.K., Crawford M.E., Errett A., Werner-Washburne M.
    J. Bacteriol. 180:6794-6794(1998)
  7. Cited for: FUNCTION, INTERACTION WITH FMP22, DISRUPTION PHENOTYPE.
  8. "Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces cerevisiae."
    Stolz J., Vielreicher M.
    J. Biol. Chem. 278:18990-18996(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases."
    Neuwirth M., Strohmeier M., Windeisen V., Wallner S., Deller S., Rippe K., Sinning I., Macheroux P., Tews I.
    FEBS Lett. 583:2179-2186(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.02 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
  10. "Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1."
    Zhang X., Teng Y.B., Liu J.P., He Y.X., Zhou K., Chen Y., Zhou C.Z.
    Biochem. J. 432:445-450(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 15-297 OF APOENZYME AND IN COMPLEXES WITH PYRIDOXAL PHOSPHATE AND GLYCERALDEHYDE 3-PHOSPHATE, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-116; LYS-117; 136-ARG-ARG-137; LYS-148; ARG-164 AND LYS-240, REACTION MECHANISM.

Entry informationi

Entry nameiSNZ1_YEAST
AccessioniPrimary (citable) accession number: Q03148
Secondary accession number(s): D6VZR9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: May 11, 2016
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  5. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  6. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.