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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)DescriptionActionsGraphical viewLength
Binding sitei23D-ribose 5-phosphateBy similarity1
Active sitei80Schiff-base intermediate with D-ribose 5-phosphateBy similarity1
Binding sitei152D-ribose 5-phosphate; via amide nitrogenBy similarity1
Binding sitei164Glyceraldehyde 3-phosphate1 Publication1
Binding sitei214D-ribose 5-phosphate; via amide nitrogenBy similarity1

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)DescriptionActionsGraphical viewLength
Mutagenesisi116E → A: No effect. 1 Publication1
Mutagenesisi117K → A: No activity. 1 Publication1
Mutagenesisi136 – 137RR → AA: No pyridoxal 5'-phosphate synthesis activity. Retains ability to isomerize dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. 1 Publication2
Mutagenesisi148K → A: No activity. 1 Publication1
Mutagenesisi164R → A: No pyridoxal 5'-phosphate synthesis activity. Retains ability to isomerize dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. 1 Publication1
Mutagenesisi240K → A: No effect. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001093581 – 297Pyridoxal 5'-phosphate synthase subunit SNZ1Add BLAST297

Proteomic databases

MaxQBiQ03148.
PRIDEiQ03148.

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. 41 interactors.
DIPiDIP-1643N.
IntActiQ03148. 9 interactors.
MINTiMINT-386894.

Structurei

Secondary structure

1297
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 14Combined sources11
Turni15 – 18Combined sources4
Beta strandi20 – 26Combined sources7
Helixi27 – 36Combined sources10
Beta strandi39 – 43Combined sources5
Helixi48 – 52Combined sources5
Turni53 – 55Combined sources3
Helixi63 – 70Combined sources8
Beta strandi77 – 82Combined sources6
Helixi86 – 94Combined sources9
Beta strandi98 – 103Combined sources6
Helixi117 – 119Combined sources3
Beta strandi124 – 130Combined sources7
Helixi131 – 140Combined sources10
Beta strandi143 – 147Combined sources5
Beta strandi151 – 153Combined sources3
Helixi157 – 174Combined sources18
Helixi179 – 189Combined sources11
Helixi193 – 202Combined sources10
Beta strandi209 – 211Combined sources3
Helixi218 – 226Combined sources9
Beta strandi232 – 234Combined sources3
Helixi236 – 240Combined sources5
Beta strandi241 – 243Combined sources3
Helixi244 – 256Combined sources13
Turni257 – 259Combined sources3
Helixi261 – 268Combined sources8
Helixi280 – 282Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ03148.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni235 – 236D-ribose 5-phosphate bindingBy similarity2

Sequence similaritiesi

Belongs to the PdxS/SNZ family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000018460.
HOGENOMiHOG000227586.
InParanoidiQ03148.
KOiK06215.
OMAiSHASNGV.
OrthoDBiEOG092C3P5O.

Family and domain databases

CDDicd04727. pdxS. 1 hit.
Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
IPR033755. PdxS/SNZ_N.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35271. 41 interactors.
DIPiDIP-1643N.
IntActiQ03148. 9 interactors.
MINTiMINT-386894.

2D gel databases

UCD-2DPAGEQ03148.

Proteomic databases

MaxQBiQ03148.
PRIDEiQ03148.

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.
OMAiSHASNGV.
OrthoDBiEOG092C3P5O.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ03148.
PROiQ03148.

Family and domain databases

CDDicd04727. pdxS. 1 hit.
Gene3Di3.20.20.70. 2 hits.
HAMAPiMF_01824. PdxS. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001852. PdxS/SNZ.
IPR033755. PdxS/SNZ_N.
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...

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: November 30, 2016
This is version 134 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.