Top Level Name

  ⌊ Superfamily (extended) Radical SAM Phosphomethylpyrimidine Synthase

    ⌊ Subgroup phosphomethylpyrimidine synthase (ThiC)

     ⌊ Family phosphomethylpyrimidine synthase (ThiC)

  ⌊ FunctionalDomain phosphomethylpyrimidine synthase (ThiC) (ID 1888714)

Superfamily Assignment Evidence Code(s) IEA
Family Assignment Evidence Code IEA
This entry was last updated onJune 24, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Caulobacter segnis Taxon ID: 88688 502843583 WP_013078559.1 (RefSeq)
Caulobacter segnis ATCC 21756 Taxon ID: 509190 295430720 ADG09892.1 (Genbank) URP

Sequence

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

1       10        20        30        40        50        60

MNIQTTIKSVAETISTGPIPGSRKVYQAGELFPDLRVPFREVAVHPSANEPPVTVYDPSG
PYTDPTVAIDIEKGLPRTREAFVVARGDVELVTDPRQVKPEDNGFAQGKHLAPEFPDQGR
KIYRAKPGKLVTQLEYARAGVITAEMEYVAIRENLRREQNAPCVRDGDDFGASIPDFVTP
EFVRQEVARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWAT
RWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLI
EQCEQGVDYFTIHAGVRLPFVPLTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFEDIC
EIMRAYDVSFSLGDGLRPGSTADANDEAQFAELRTLGELTKVAWSHGVQVMIEGPGHVAM
HKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKE
HLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLALDPE
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
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
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
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
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, 2:22 a.m. update curation agent updateSuperfamily.py setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.