Structure of PDB 3kvv Chain B

Receptor sequence

>3kvvB (length=243) Species: 83333 (Escherichia coli K-12)

KSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTT
WRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHI
NVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTH
VGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATL
LTMCASQGLRAGMVAGVIVNRTQMKQTESHAVKIVVEAARRLL

3D structure

• PDB: 3kvv Glycal formation in crystals of uridine phosphorylase.
• Chain: B
• Resolution: 1.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H8 G26 R30 R48 E80 R91 T94 R168 I220 V221 R223
• Catalytic site (residue number reindexed from 1): H6 G24 R28 R46 E78 R89 T92 R166 I218 V219 R221
• 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	URF	B	T95 G96 F162 Q166 I220 V221	T93 G94 F160 Q164 I218 V219
BS02	SO4	B	G26 R30 R91 G93 T94	G24 R28 R89 G91 T92
BS03	R2B	B	R91 T94 E196 M197 E198	R89 T92 E194 M195 E196

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004850 uridine phosphorylase activity
• GO:0005524 ATP binding
• GO:0016757 glycosyltransferase activity
• GO:0016763 pentosyltransferase activity
• GO:0030955 potassium ion binding
• GO:0042802 identical protein binding
• GO:0047847 deoxyuridine phosphorylase activity

Biological Process

• GO:0006218 uridine catabolic process
• GO:0006974 DNA damage response
• GO:0009116 nucleoside metabolic process
• GO:0009164 nucleoside catabolic process
• GO:0009166 nucleotide catabolic process
• GO:0044206 UMP salvage
• GO:0046050 UMP catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:3kvv, PDBe:3kvv, PDBj:3kvv
• PDBsum: 3kvv
• PubMed: 20364833
• UniProt: P12758|UDP_ECOLI Uridine phosphorylase (Gene Name=udp)