Top Level Name

  ⌊ Superfamily (extended) Radical SAM Phosphomethylpyrimidine Synthase

    ⌊ Subgroup phosphomethylpyrimidine synthase (ThiC)

     ⌊ Family phosphomethylpyrimidine synthase (ThiC)

  ⌊ FunctionalDomain Phosphomethylpyrimidine synthase (ThiC) (ID 396475)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code ISS PubMed:18953358
This entry was last updated onJune 24, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Caulobacter crescentus CB15 Taxon ID: 190650 16126272 NP_420836.1 (RefSeq) URP
Caulobacter vibrioides Taxon ID: 155892 499222355 WP_010919895.1 (RefSeq) URP
Caulobacter crescentus NA1000 Taxon ID: 565050 221235046 YP_002517482.1 (RefSeq) URP
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Uniprot

Protein NameAccessionEC Number Identifier
Phosphomethylpyrimidine synthase {ECO:0000255|HAMAP-Rule:MF_00089} B8GX84 THIC_CAUCN (Swiss-Prot)
Phosphomethylpyrimidine synthase Q9A6Q5 THIC_CAUCR (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 612 | Length of Functional Domain: 612

1       10        20        30        40        50        60

MNIQSTIKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSG
PYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGR
KIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTP
EFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWAT
RWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLI
EQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEIC
EIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAM
HKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKE
HLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPE
TARKFHDETLPKEAHKTAHFCSMCGPKFCSMKISQEVRDFAAGKAPNSAELGMAEMSEKF
REQGSEIYLKTE
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues

Subgroup CAR This EFD conserves 3/3 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
561 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IEA
564 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IEA
569 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IEA
Family CAR This EFD conserves 5/5 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
417 His (H) side chain Binds Zn(II) ion metal ligand -- binding IDA PubMed:24161603
481 His (H) side chain Binds Zn(II) ion metal ligand -- binding IDA PubMed:24161603
561 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:24161603
564 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:24161603
569 Cys (C) side chain Binds [4Fe-4S]-AdoMet cluster cofactor binding -- binding IDA PubMed:24161603

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
3EPN Crystal Structure Of Caulobacter Crescentus Thic Complexed With Imidazole Ribonucleotide Thiamine Biosynthesis Protein Thic 6 2.11 1-(5-O-Phosphono-Beta-D-Ribofuranosyl)-1H-Imidazole CSA • PDB • PDBSum
3EPO Crystal Structure Of Caulobacter Crescentus Thic Complexed With Hmp-P Thiamine Biosynthesis Protein Thic 6 2.1 (4-Amino-2-Methylpyrimidin-5-Yl)Methyl Dihydrogen Phosphate CSA • PDB • PDBSum
4S2A Crystal Structure Of Caulobacter Crescentus Thic With Fe4S4 Cluster At Remote Site (Holo Form) Phosphomethylpyrimidine Synthase 6 2.93 Iron/Sulfur Cluster • Phosphate Ion CSA • PDB • PDBSum
3EPM Crystal Structure Of Caulobacter Crescentus Thic Thiamine Biosynthesis Protein Thic 3 2.79 Selenomethionine
(3 more ⇓) 		CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
July 29, 2014, 2:21 a.m. update curation agent holliday setDomainBoundaries.py
Sept. 29, 2014, 2:24 a.m. update curation agent setDomainBoundaries.py holliday
update family assignment evidence code CFM,ISS ISS
Oct. 30, 2014, 2:53 p.m. update curation agent holliday setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.