Structure of PDB 4r2w Chain D

Receptor sequence

>4r2wD (length=251) Species: 211586 (Shewanella oneidensis MR-1)

ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSY
LAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVN
VGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHI
GVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLF
TMCATQGWRAACVAGVIVNRTQQEIPDEATMKKTEVSAVSIVVAAAKKLL
A

3D structure

• PDB: 4r2w High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.
• Chain: D
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H5 G23 R27 R45 E77 R88 T91 R165 I217 V218 R220 M231
• Catalytic site (residue number reindexed from 1): H5 G23 R27 R45 E77 R88 T91 R165 I217 V218 R220 M231
• Enzyme Commision number: 2.4.2.3: uridine phosphorylase.

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	SO4	D	G23 R27 R88 G90 T91	G23 R27 R88 G90 T91
BS02	GOL	D	T91 M194 E195	T91 M194 E195
BS03	GOL	D	N130 A204	N130 A204

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004850 uridine phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0016763 pentosyltransferase activity
• GO:0047847 deoxyuridine phosphorylase activity

Biological Process

• GO:0009116 nucleoside metabolic process
• GO:0009164 nucleoside catabolic process
• GO:0009166 nucleotide catabolic process
• GO:0044206 UMP salvage

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4r2w, PDBe:4r2w, PDBj:4r2w
• PDBsum: 4r2w
• PubMed: 25478848
• UniProt: Q8E9X9