Structure of PDB 3b9x Chain D

Receptor sequence
>3b9xD (length=307) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVAGNQTLDKTLINGLN
VCQKLEINVPVYAGMPQPIMRQQIVAIHGDTGLDGPVFEPLTRQAESTHA
VKYIIDTLMASDGDITLVPVGPLSNIAVAMRMQPAILPKIREIVLMGGAY
GTGNFTPSAEFNIFADPEAARVVFTSGVPLVMMGLDLTNQTVCTPDVIAR
MERAGGPAGELFSDIMNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIK
TQEMYVEVDVNSGPCYGRTVCDELGVLGKPANTKVGITIDTDWFWGLVEE
CVRGYIK
3D structure
PDB3b9x Structural basis for substrate specificity in group I nucleoside hydrolases
ChainD
Resolution2.3 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D11 D16 N40 Q75 V124 F165 N166 H239 D240
Catalytic site (residue number reindexed from 1) D9 D14 N38 Q73 V120 F161 N162 H235 D236
Enzyme Commision number 3.2.2.8: ribosylpyrimidine nucleosidase.
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 CA D D11 D16 V124 D240 D9 D14 V120 D236
BS02 NOS D D15 N40 I81 H82 M150 E164 F165 N166 Q227 Y231 H239 D240 D13 N38 I77 H78 M146 E160 F161 N162 Q223 Y227 H235 D236
Gene Ontology
Molecular Function
GO:0005509 calcium ion binding
GO:0008477 purine nucleosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0042802 identical protein binding
GO:0045437 uridine nucleosidase activity
GO:0046872 metal ion binding
GO:0050263 ribosylpyrimidine nucleosidase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006152 purine nucleoside catabolic process
GO:0006206 pyrimidine nucleobase metabolic process
GO:0046133 pyrimidine ribonucleoside catabolic process
GO:0051289 protein homotetramerization
Cellular Component
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Cellular Component
External links
PDB RCSB:3b9x, PDBe:3b9x, PDBj:3b9x
PDBsum3b9x
PubMed18361502
UniProtP33022|RIHB_ECOLI Pyrimidine-specific ribonucleoside hydrolase RihB (Gene Name=rihB)

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