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Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose

X-ray diffraction
1.78Å resolution
PDB entry 1yoe coloured by chain, front view.
PDB entry 1yoe coloured by chain, side view.
PDB entry 1yoe coloured by chain, top view.
Source organism: Escherichia coli
Assemblies composition:
homo tetramer
homo dimer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: Pyrimidine-specific ribonucleoside hydrolase RihA
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Multimeric state: homo tetramer
Accessible surface area: 44269.94 Å2
Buried surface area: 7666.52 Å2
Dissociation area: 2,909.26 Å2
Dissociation energy (ΔGdiss): -0.35 kcal/mol
Dissociation entropy (TΔSdiss): 41.29 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-154394
Assembly 2 (preferred)
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Assembly Name: Pyrimidine-specific ribonucleoside hydrolase RihA
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Multimeric state: homo dimer
Accessible surface area: 23312.68 Å2
Buried surface area: 2655.56 Å2
Dissociation area: 865.78 Å2
Dissociation energy (ΔGdiss): 1.47 kcal/mol
Dissociation entropy (TΔSdiss): 13.27 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-154393
Assembly 3
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Assembly Name: Pyrimidine-specific ribonucleoside hydrolase RihA
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Multimeric state: homo dimer
Accessible surface area: 23312.68 Å2
Buried surface area: 2655.56 Å2
Dissociation area: 865.78 Å2
Dissociation energy (ΔGdiss): 1.47 kcal/mol
Dissociation entropy (TΔSdiss): 13.27 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-154393
Assembly 4
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Assembly Name: Pyrimidine-specific ribonucleoside hydrolase RihA
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Multimeric state: homo tetramer
Accessible surface area: 41616.79 Å2
Buried surface area: 10319.67 Å2
Dissociation area: 1,738.67 Å2
Dissociation energy (ΔGdiss): 14.15 kcal/mol
Dissociation entropy (TΔSdiss): 14.98 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-154394

Macromolecules

Pyrimidine-specific ribonucleoside hydrolase RihA
Chain: A
Length: 322 amino acids
Theoretical weight: 35.13 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P41409 (Residues: 2-311; Coverage: 100%)
Gene names: JW0646, b0651, rihA, ybeK
Pfam: Inosine-uridine preferring nucleoside hydrolase
InterPro:
CATH: Ribonucleoside hydrolase-like
Pyrimidine-specific ribonucleoside hydrolase RihA in PDB entry 1yoe, assembly 2, front view.
Pyrimidine-specific ribonucleoside hydrolase RihA in PDB entry 1yoe, assembly 2, side view.
Pyrimidine-specific ribonucleoside hydrolase RihA in PDB entry 1yoe, assembly 2, top view.
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