Structure of PDB 4s25 Chain A

Receptor sequence

>4s25A (length=513) Species: 3702 (Arabidopsis thaliana)

SPDFQPIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFD
NYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEM
LYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNAN
IGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAV
PVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLR
YIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVA
LSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVP
MHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALG
TALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDA
LSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFC
SMKITEDIRKYAE

3D structure

• PDB: 4s25 Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
• Chain: A
• Resolution: 1.45 Å

Enzymatic activity

• Enzyme Commision number: 4.1.99.17: phosphomethylpyrimidine synthase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SF4	A	W538 C570 M572 C573 C578 S579 M580	W460 C492 M494 C495 C500 S501 M502
BS02	IRN	A	N228 M257 Y286 H322 S342 R343 D383 R386 E422 G423 Y449	N150 M179 Y208 H244 S264 R265 D305 R308 E344 G345 Y371
BS03	SAH	A	N228 G230 L259 V341 R343 R386 H426 E489 H490 L493 P494	N150 G152 L181 V263 R265 R308 H348 E411 H412 L415 P416
BS04	ZN	A	H426 H490	H348 H412

Gene Ontology

Molecular Function

• GO:0016830 carbon-carbon lyase activity
• GO:0051536 iron-sulfur cluster binding

Biological Process

• GO:0009228 thiamine biosynthetic process

External links

• PDB: RCSB:4s25, PDBe:4s25, PDBj:4s25
• PDBsum: 4s25
• PubMed: 25813242
• UniProt: O82392|THIC_ARATH Phosphomethylpyrimidine synthase, chloroplastic (Gene Name=THIC)