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P43534

- THI5_YEAST

UniProt

P43534 - THI5_YEAST

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Protein

4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase THI5

Gene

THI5

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

Functioni

Responsible for the formation of the pyrimidine heterocycle in the thiamine biosynthesis pathway. Catalyzes the formation of hydroxymethylpyrimidine phosphate (HMP-P) from histidine and pyridoxal phosphate (PLP). The protein uses PLP and the active site histidine to form HMP-P, generating an inactive enzyme. The enzyme can only undergo a single turnover, which suggests it is a suicide enzyme.1 Publication

Cofactori

Fe cation1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei66 – 6611 Publication

GO - Biological processi

  1. thiamine biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

Thiamine biosynthesis

Keywords - Ligandi

Iron

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER3O-3915.
YEAST:MONOMER3O-3915.
UniPathwayiUPA00060.

Names & Taxonomyi

Protein namesi
Recommended name:
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase THI51 Publication
Short name:
HMP-P synthase1 Publication
Short name:
Hydroxymethylpyrimidine phosphate synthaseCurated
Alternative name(s):
Thiamine biosynthesis protein 51 Publication
Thiamine pyrimidine synthaseBy similarity
Gene namesi
Name:THI51 Publication
Synonyms:MOL21 Publication
Ordered Locus Names:YFL058WImported
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VI

Organism-specific databases

CYGDiYFL058w.
SGDiS000001836. THI5.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi11 – 111N → A: Unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi12 – 121W → A: Unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi62 – 621K → A: Unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi66 – 661H → A: Unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi195 – 1951C → A: Attenuates the coordination of ion and is unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi196 – 1961C → A: Attenuates the coordination of ion and is unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi197 – 1971C → A: Attenuates the coordination of ion and is unable to sustain growth in thiamine-free medium. 1 Publication
Mutagenesisi199 – 1991C → A: Attenuates the coordination of ion and is unable to sustain growth in thiamine-free medium. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3403404-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase THI5PRO_0000211618Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei62 – 621N6-(pyridoxal phosphate)lysine1 Publication

Expressioni

Gene expression databases

GenevestigatoriP43534.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
RSP5P399402EBI-19221,EBI-16219

Protein-protein interaction databases

BioGridi31089. 2 interactions.
DIPiDIP-3951N.
IntActiP43534. 1 interaction.
MINTiMINT-525063.
STRINGi4932.YFL058W.

Structurei

Secondary structure

1
340
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 94Combined sources
Beta strandi11 – 133Combined sources
Helixi16 – 183Combined sources
Helixi19 – 268Combined sources
Helixi29 – 324Combined sources
Beta strandi37 – 448Combined sources
Helixi45 – 473Combined sources
Helixi48 – 547Combined sources
Beta strandi55 – 573Combined sources
Beta strandi59 – 635Combined sources
Helixi64 – 718Combined sources
Turni72 – 743Combined sources
Beta strandi77 – 848Combined sources
Beta strandi89 – 946Combined sources
Turni95 – 984Combined sources
Helixi103 – 1064Combined sources
Beta strandi110 – 1134Combined sources
Helixi117 – 12711Combined sources
Turni128 – 1303Combined sources
Beta strandi135 – 1406Combined sources
Helixi142 – 1443Combined sources
Helixi145 – 1506Combined sources
Beta strandi153 – 1608Combined sources
Turni161 – 1633Combined sources
Helixi164 – 17411Combined sources
Helixi179 – 1813Combined sources
Beta strandi182 – 1865Combined sources
Helixi196 – 1994Combined sources
Beta strandi201 – 2066Combined sources
Helixi207 – 2126Combined sources
Helixi214 – 23320Combined sources
Helixi235 – 24511Combined sources
Helixi247 – 2493Combined sources
Helixi252 – 26110Combined sources
Turni262 – 2643Combined sources
Helixi273 – 28513Combined sources
Helixi315 – 33016Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H65X-ray2.60A/B1-340[»]
4H67X-ray2.70A/B/C/D/E/F/G/H1-340[»]
4H6DX-ray2.90A/B/C/D/E/F/G/H1-340[»]
ProteinModelPortaliP43534.
SMRiP43534. Positions 4-338.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni115 – 1184Pyridoxal phosphate binding1 Publication

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi195 – 1995CCCFC; essential for catalytic activity, may be the site of iron coordination1 Publication

Sequence similaritiesi

Belongs to the NMT1/THI5 family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000017029.
HOGENOMiHOG000160891.
InParanoidiP43534.
KOiK18278.
OMAiEIEMIEP.
OrthoDBiEOG7DRJD1.

Family and domain databases

InterProiIPR027939. NMT1/THI5.
IPR015168. SsuA/THI5.
[Graphical view]
PANTHERiPTHR31528. PTHR31528. 1 hit.
PfamiPF09084. NMT1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P43534-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSTDKITFLL NWQPTPYHIP IFLAQTKGYF KEQGLDMAIL EPTNPSDVTE
60 70 80 90 100
LIGSGKVDMG LKAMIHTLAA KARGFPVTSV ASLLDEPFTG VLYLKGSGIT
110 120 130 140 150
EDFQSLKGKK IGYVGEFGKI QIDELTKHYG MKPEDYTAVR CGMNVAKYII
160 170 180 190 200
EGKIDAGIGI ECMQQVELEE YLAKQGRPAS DAKMLRIDKL ACLGCCCFCT
210 220 230 240 250
VLYICNDEFL KKNPEKVRKF LKAIKKATDY VLADPVKAWK EYIDFKPQLN
260 270 280 290 300
NDLSYKQYQR CYAYFSSSLY NVHRDWKKVT GYGKRLAILP PDYVSNYTNE
310 320 330 340
YLSWPEPEEV SDPLEAQRLM AIHQEKCRQE GTFKRLALPA
Length:340
Mass (Da):38,592
Last modified:November 1, 1995 - v1
Checksum:iD810C5D5A86FA6C0
GO

Mass spectrometryi

Molecular mass is 38513.4 Da from positions 1 - 340. Determined by ESI. This mass is that of the untagged protein plus the mass of an iron ion.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48220 Genomic DNA. Translation: CAA88253.1.
D50617 Genomic DNA. Translation: BAA09183.1.
BK006940 Genomic DNA. Translation: DAA12382.1.
RefSeqiNP_116597.1. NM_001179909.1.

Genome annotation databases

EnsemblFungiiYFL058W; YFL058W; YFL058W.
GeneIDi850486.
KEGGisce:YFL058W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48220 Genomic DNA. Translation: CAA88253.1 .
D50617 Genomic DNA. Translation: BAA09183.1 .
BK006940 Genomic DNA. Translation: DAA12382.1 .
RefSeqi NP_116597.1. NM_001179909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4H65 X-ray 2.60 A/B 1-340 [» ]
4H67 X-ray 2.70 A/B/C/D/E/F/G/H 1-340 [» ]
4H6D X-ray 2.90 A/B/C/D/E/F/G/H 1-340 [» ]
ProteinModelPortali P43534.
SMRi P43534. Positions 4-338.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31089. 2 interactions.
DIPi DIP-3951N.
IntActi P43534. 1 interaction.
MINTi MINT-525063.
STRINGi 4932.YFL058W.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YFL058W ; YFL058W ; YFL058W .
GeneIDi 850486.
KEGGi sce:YFL058W.

Organism-specific databases

CYGDi YFL058w.
SGDi S000001836. THI5.

Phylogenomic databases

GeneTreei ENSGT00390000017029.
HOGENOMi HOG000160891.
InParanoidi P43534.
KOi K18278.
OMAi EIEMIEP.
OrthoDBi EOG7DRJD1.

Enzyme and pathway databases

UniPathwayi UPA00060 .
BioCyci MetaCyc:MONOMER3O-3915.
YEAST:MONOMER3O-3915.

Miscellaneous databases

NextBioi 966152.

Gene expression databases

Genevestigatori P43534.

Family and domain databases

InterProi IPR027939. NMT1/THI5.
IPR015168. SsuA/THI5.
[Graphical view ]
PANTHERi PTHR31528. PTHR31528. 1 hit.
Pfami PF09084. NMT1. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Characterisation of a new thiamine regulated Saccharomyces cerevisiae gene, THI5."
    Hather R.J., Praekelt U., Meacock P.A.
    Submitted (FEB-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "Pyrimidine moiety of thiamin is biosynthesized from pyridoxine and histidine in Saccharomyces cerevisiae."
    Tazuya K., Azumi C., Yamada K., Kumaoka H.
    Biochem. Mol. Biol. Int. 36:883-888(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: THIAMINE BIOSYNTHESIS IN YEAST.
  5. "The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine."
    Wightman R., Meacock P.A.
    Microbiology 149:1447-1460(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PATHWAY.
  6. "The direct precursor of the pyrimidine moiety of thiamin is not urocanic acid but histidine in Saccharomyces cerevisiae."
    Ishida S., Tazuya-Murayama K., Kijima Y., Yamada K.
    J. Nutr. Sci. Vitaminol. 54:7-10(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: THIAMINE BIOSYNTHESIS IN YEAST.
  7. "The last piece in the vitamin B1 biosynthesis puzzle: structural and functional insight into yeast 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase."
    Coquille S., Roux C., Fitzpatrick T.B., Thore S.
    J. Biol. Chem. 287:42333-42343(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE, SUBUNIT, COFACTOR, MASS SPECTROMETRY, MUTAGENESIS OF ASN-11; TRP-12; LYS-62 AND HIS-66.

Entry informationi

Entry nameiTHI5_YEAST
AccessioniPrimary (citable) accession number: P43534
Secondary accession number(s): D6VTH2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: January 7, 2015
This is version 101 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, 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. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome VI
    Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

External Data

Dasty 3

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 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.