Structure of PDB 5oln Chain B

Receptor sequence

>5olnB (length=434) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

AMRMVDIIIKKQNGKELTTEEIQFFVNGYTDGSIPDYQASALAMAIFFQD
MSDRERADLTMAMVNSGETIDLSAIEGIKVDKHSTGGVGDTTTLVLAPLV
AALDVPVAKMSGRGLGHTGGTIDKLEAIMGFHVELTKDEFIKLVNRDKVA
VIGQSGNLTPADKKLYALRDVTGTVNSIPLIASSIMSKKIAAGADAIVLD
VKTGAGAFMKTEEDAAELAKAMVRIGNNVGRQTMAVISDMSQPLGFAIGN
ALEVKEAIDTLKGEGPEDLHELVLTLGSQMVVLAKKADTLDEARAKLEEV
MKNGKALEKFKDFLKNQGGDSSIVDDPSKLPQAAYQIDVPAKEAGVVSEI
VADEIGVAAMLLGAGRATKEDEIDLAVGIMLRKKVGDKVEKGEPLVTLYA
NRENVDEVIAKVYDNIRIAAEAKAPKLIHTLITE

3D structure

• PDB: 5oln Crystal structure of pyrimidine-nucleoside phosphorylase from Bacillus subtilis in complex with imidazole and sulfate.
• Chain: B
• Resolution: 1.88 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H82 D161 R168 S183 K187
• Catalytic site (residue number reindexed from 1): H83 D162 R169 S184 K188
• Enzyme Commision number: 2.4.2.2: pyrimidine-nucleoside 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	IMD	B	Y165 R168 I180 S183	Y166 R169 I181 S184
BS02	SO4	B	T92 S110 T120	T93 S111 T121

Gene Ontology

Molecular Function

• GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
• GO:0004850 uridine phosphorylase activity
• GO:0009032 thymidine phosphorylase activity
• GO:0016154 pyrimidine-nucleoside phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0016763 pentosyltransferase activity
• GO:0046872 metal ion binding
• GO:0047847 deoxyuridine phosphorylase activity

Biological Process

• GO:0006206 pyrimidine nucleobase metabolic process
• GO:0006213 pyrimidine nucleoside metabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5oln, PDBe:5oln, PDBj:5oln
• PDBsum: 5oln
• PubMed: 29633966
• UniProt: P39142|PDP_BACSU Pyrimidine-nucleoside phosphorylase (Gene Name=pdp)