Q89FP0 · THIC_BRADU
- ProteinPhosphomethylpyrimidine synthase
- GenethiC
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids632 (go to sequence)
- Protein existenceInferred from homology
- Annotation score3/5
Function
function
Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.
Catalytic activity
- 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-deoxyadenosine + CO + formate + 3 H+ + L-methionine
Cofactor
Note: Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Pathway
Cofactor biosynthesis; thiamine diphosphate biosynthesis.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 221 | substrate | ||||
Sequence: N | ||||||
Binding site | 250 | substrate | ||||
Sequence: M | ||||||
Binding site | 279 | substrate | ||||
Sequence: Y | ||||||
Binding site | 315 | substrate | ||||
Sequence: H | ||||||
Binding site | 335-337 | substrate | ||||
Sequence: SRG | ||||||
Binding site | 376-379 | substrate | ||||
Sequence: DGLR | ||||||
Binding site | 415 | substrate | ||||
Sequence: E | ||||||
Binding site | 419 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 442 | substrate | ||||
Sequence: Y | ||||||
Binding site | 483 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 563 | [4Fe-4S] cluster (UniProtKB | ChEBI); 4Fe-4S-S-AdoMet | ||||
Sequence: C | ||||||
Binding site | 566 | [4Fe-4S] cluster (UniProtKB | ChEBI); 4Fe-4S-S-AdoMet | ||||
Sequence: C | ||||||
Binding site | 571 | [4Fe-4S] cluster (UniProtKB | ChEBI); 4Fe-4S-S-AdoMet | ||||
Sequence: C |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Molecular Function | 4 iron, 4 sulfur cluster binding | |
Molecular Function | carbon-carbon lyase activity | |
Molecular Function | zinc ion binding | |
Biological Process | thiamine biosynthetic process | |
Biological Process | thiamine diphosphate biosynthetic process |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended namePhosphomethylpyrimidine synthase
- EC number
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageBacteria > Pseudomonadota > Alphaproteobacteria > Hyphomicrobiales > Nitrobacteraceae > Bradyrhizobium
Accessions
- Primary accessionQ89FP0
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000152790 | 1-632 | Phosphomethylpyrimidine synthase | |||
Sequence: MNIRSNPQQTVPAVTTGPLSSSRKIFASPDAAPDLRVPLREIILSEGAGEPNLPVYDTSGPYTDPSVTIDVNAGLARSRKQWVLERGGVEEYEGRQVKPEDNGNLSTDKAARAFSAYHKPLRGLDGHKITQLEFARAGIITKEMIYVAARENLGRKEQLERAEAALADGESFGAEVPAFITPEFVRSEIARGRAIIPCNINHSELEPMIIGRNFLTKINANIGNSAVTSSVEEEVEKMVWAIRWGADTVMDLSTGRNIHTTREWILRNAPVPIGTVPIYQALEKCNGDPVKLTWELYKDTLIEQCEQGVDYFTIHAGVRLSYIHLTANRVTGIVSRGGSIMAKWCLAHHKESFLYTHFDEICDLMRKYDVSFSLGDGLRPGSIADANDRAQFAELETLGELTKIAWDKGCQVMIEGPGHVPMHKIKINMDKQLRECGEAPFYTLGPLTTDIAPGYDHITSGIGAAMIGWFGCAMLCYVTPKEHLGLPDRNDVKVGVITYKIAAHASDLAKGHPAAQLRDDALSRARFDFRWSDQFNLGLDPDTAKNFHDETLPKEAHKVAHFCSMCGPKFCSMKITQDVRDYAATLNDPNSIGMSLSGTAEDGMKQMSAKFKEMGSSVYLDAEKVKESNRVL |
Interaction
Structure
Family & Domains
Features
Showing features for compositional bias, region.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-23 | Polar residues | ||||
Sequence: MNIRSNPQQTVPAVTTGPLSSSR | ||||||
Region | 1-26 | Disordered | ||||
Sequence: MNIRSNPQQTVPAVTTGPLSSSRKIF |
Sequence similarities
Belongs to the ThiC family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length632
- Mass (Da)69,760
- Last updated2003-06-01 v1
- Checksum6BAD3DAF91D99895
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-23 | Polar residues | ||||
Sequence: MNIRSNPQQTVPAVTTGPLSSSR |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
BA000040 EMBL· GenBank· DDBJ | BAC51924.1 EMBL· GenBank· DDBJ | Genomic DNA |