Structure of PDB 4s26 Chain B

Receptor sequence

>4s26B (length=512) Species: 3702 (Arabidopsis thaliana)

PIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFDNYDTS
GPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEMLYCAT
REKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNANIGNSA
VASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAVPVGTV
PIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLRYIPLT
AKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVALSIGD
GLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVPMHKIP
ENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALGTALLC
YVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDALSKAR
FEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFCSMKIT
EDIRKYAEENGY

3D structure

• PDB: 4s26 Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
• Chain: B
• Resolution: 1.85 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	B	W538 C570 M572 C573 C578 S579 M580	W455 C487 M489 C490 C495 S496 M497
BS02	IRN	B	N228 M257 Y286 H322 S342 R343 G344 R386 E422 G423 Y449	N145 M174 Y203 H239 S259 R260 G261 R303 E339 G340 Y366
BS03	SAH	B	N228 I229 G230 L259 V341 R343 R386 H426 E489 H490 L493 P494	N145 I146 G147 L176 V258 R260 R303 H343 E406 H407 L410 P411
BS04	ZN	B	H426 H490	H343 H407

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:4s26, PDBe:4s26, PDBj:4s26
• PDBsum: 4s26
• PubMed: 25813242
• UniProt: O82392|THIC_ARATH Phosphomethylpyrimidine synthase, chloroplastic (Gene Name=THIC)