THI5 (YFL058W) encodes a 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMP-P) synthase of the NMT1/THI5 family, which makes the pyrimidine half of thiamine. The iron-dependent homodimeric enzyme binds pyridoxal 5'-phosphate as a substrate (via an active-site lysine) and builds HMP-P from it and the side chain of one of its own histidine residues, which inactivates the enzyme after a single turnover. Its fold combines features of periplasmic binding proteins and PLP-dependent enzymes. THI5 is one of four almost identical subtelomeric paralogues (THI5, THI11, THI12, THI13) that are functionally redundant for aerobic HMP synthesis from the vitamin B6 pathway; the quadruple mutant requires thiamine or HMP under aerobic conditions. The family is induced by thiamine limitation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003674 molecular_function | ND GO_REF:0000015 | MODIFY | Summary: Root MF with ND ("no data") is outdated: the HMP-P synthase activity of Thi5 has since been demonstrated (PMID:23048037) and is annotated as GO:0106344. Reason: Molecular function is now known. Proposed replacements: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP Supporting Evidence: PMID:23048037 We report a structure-function study of the HMP-P synthase from yeast, THI5p |
| GO:0005506 iron ion binding | IDA PMID:23048037 The last piece in the vitamin B1 biosynthesis puzzle: struct... | ACCEPT | Summary: Iron binding is essential for HMP-P synthesis by Thi5p, and the purified protein carries bound iron by mass spectrometry (PMID:23048037). Reason: Experimentally supported cofactor binding required for the core activity. Supporting Evidence: PMID:23048037 we could show that iron binding to HMP-P synthase is essential for the reaction |
| GO:0005515 protein binding | IPI PMID:16606443 Comparative analysis of Saccharomyces cerevisiae WW domains ... | REMOVE | Summary: Binding to the Rsp5 WW domains on a protein microarray (PMID:16606443), one of 587 interactions in a high-throughput WW-domain screen. No functional consequence for Thi5 is known and protein binding is uninformative. Reason: Uninformative protein binding from a high-throughput screen with no more specific supported MF; removal does not imply the interaction is false. Supporting Evidence: PMID:16606443 We observed 587 interactions between these 12 domains and 207 proteins, most of which have not previously been described |
| GO:0005515 protein binding | IPI PMID:23048037 The last piece in the vitamin B1 biosynthesis puzzle: struct... | MODIFY | Summary: Self-interaction (Thi5-Thi5) from the crystal structure and solution analysis showing that Thi5p is a homodimer (PMID:23048037). Protein binding is uninformative; the self-association is better described as homodimerization. Reason: The interaction partner is Thi5 itself; homodimerization activity is the informative term. Proposed replacements: protein homodimerization activity Supporting Evidence: file:yeast/THI5/THI5-uniprot.txt SUBUNIT: Homodimer. |
| GO:0005575 cellular_component | ND GO_REF:0000015 | ACCEPT | Summary: No experimental localisation exists for Thi5 (the paralogues are nearly identical, which complicates tagging studies). The enzyme is presumed cytosolic but this has not been shown; the ND statement remains accurate. Reason: Accurately records the absence of localisation data. Supporting Evidence: PMID:12777485 The THI5 gene family of Saccharomyces cerevisiae comprises four highly conserved members |
| GO:0009228 thiamine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA (PTN001267680) with S. pombe nmt1, C. albicans THI5 and the four S. cerevisiae paralogues as descendants. Correct; Thi5 makes the pyrimidine moiety. Reason: Core BP. Supporting Evidence: PMID:12777485 functionally redundant in terms of HMP formation for thiamin biosynthesis |
| GO:0009228 thiamine biosynthetic process | IDA PMID:23048037 The last piece in the vitamin B1 biosynthesis puzzle: struct... | ACCEPT | Summary: Structure-function and complementation analysis of Thi5p HMP-P synthase (PMID:23048037). Thi5 performs the pyrimidine-forming step of thiamine synthesis. Reason: Core BP. Supporting Evidence: PMID:23048037 Mutational and yeast complementation studies identify the key residues for HMP-P biosynthesis |
| GO:0009228 thiamine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/InterPro (IPR027939, NMT1/THI5 family) mapping to thiamine biosynthesis; correct. Reason: Core BP. Supporting Evidence: PMID:12777485 functionally redundant in terms of HMP formation for thiamin biosynthesis |
| GO:0009228 thiamine biosynthetic process | IGI PMID:12777485 The THI5 gene family of Saccharomyces cerevisiae: distributi... | ACCEPT | Summary: Combinatorial deletion of THI5 with THI13 (SGD:S000002403) and the other paralogues shows redundancy for HMP formation (PMID:12777485). Reason: Core BP; genetic redundancy evidence. Supporting Evidence: PMID:12777485 all combinations of the single, double, triple and quadruple deletion mutants were constructed |
| GO:0009228 thiamine biosynthetic process | IGI PMID:12777485 The THI5 gene family of Saccharomyces cerevisiae: distributi... | ACCEPT | Summary: Genetic interaction with THI11 (SGD:S000003917) in the combinatorial deletion series (PMID:12777485). Reason: Core BP; genetic redundancy evidence. Supporting Evidence: PMID:12777485 functionally redundant in terms of HMP formation for thiamin biosynthesis |
| GO:0009228 thiamine biosynthetic process | IGI PMID:12777485 The THI5 gene family of Saccharomyces cerevisiae: distributi... | ACCEPT | Summary: Genetic interaction with THI12 (SGD:S000005276) in the combinatorial deletion series (PMID:12777485). Reason: Core BP; genetic redundancy evidence. Supporting Evidence: PMID:12777485 each promotes synthesis of HMP from the pyridoxine (vitamin B(6)) biosynthetic pathway |
| GO:0009229 thiamine diphosphate biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: UniPathway UPA00060 (thiamine diphosphate biosynthesis) mapping. HMP-P is a precursor of ThDP, so this is correct; thiamine biosynthesis is the more direct process. Reason: Correct pathway assignment. Supporting Evidence: file:yeast/THI5/THI5-uniprot.txt PATHWAY: Cofactor biosynthesis; thiamine diphosphate biosynthesis. |
| GO:0106344 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP | IDA PMID:23048037 The last piece in the vitamin B1 biosynthesis puzzle: struct... | ACCEPT | Summary: Thi5p structure and mutagenesis establish HMP-P synthesis from PLP (as substrate) and histidine, requiring iron (PMID:23048037). The Candida orthologue reconstitution confirmed His66 as the histidine source (PMID:22568620). Reason: Core MF. Supporting Evidence: PMID:23048037 the use of pyridoxal 5'-phosphate as a substrate rather than as a cofactor PMID:22568620 Our data suggest that His66 of the THI5 protein is the histidine source for pyrimidine formation and that the pyrimidine synthase is a single-turnover enzyme |
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Download this section (compressed HTML)Q: Do the four THI5-family paralogues differ in expression conditions or in turnover (e.g. Rsp5-dependent degradation of spent enzyme) in a way that explains retention of four nearly identical copies?
Experiment: Measure protein levels and half-lives of individually tagged THI5, THI11, THI12 and THI13 under thiamine limitation, and test whether spent (His-modified) enzyme is ubiquitinated by Rsp5 and degraded.
Protein involved in synthesis of the thiamine precursor HMP; member of a subtelomeric gene family including THI5, THI11, THI12, and THI13; hydroxymethylpyrimidine is also known as HMP
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