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Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAM binding

X-ray diffraction
2.6Å resolution
PDB entry 3v8v coloured by chain, front view.
PDB entry 3v8v coloured by chain, side view.
PDB entry 3v8v coloured by chain, top view.
Source organism: Escherichia coli K-12
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Ribosomal RNA large subunit methyltransferase K/L
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Multimeric state: monomeric
Accessible surface area: 30286.11 Å2
Buried surface area: 313.86 Å2
Dissociation area: 156.93 Å2
Dissociation energy (ΔGdiss): -2.88 kcal/mol
Dissociation entropy (TΔSdiss): 2.28 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-160015
Monomeric assembly 1 of PDB entry 3v8v coloured by chemically distinct molecules, front view.
Monomeric assembly 1 of PDB entry 3v8v coloured by chemically distinct molecules, side view.
Monomeric assembly 1 of PDB entry 3v8v coloured by chemically distinct molecules, top view.
    Assembly 1
Confidence : 95%
No. subunits : 1
Symmetry : None
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3DComplex & QSbio predictionx
No. subunits : 1
Symmetry : None
Evidence : This biological assembly agrees with the prediction of both PISA & EPPIC
Assembly 2
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Assembly Name: Ribosomal RNA large subunit methyltransferase K/L
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Multimeric state: monomeric
Accessible surface area: 28818.01 Å2
Buried surface area: 313.28 Å2
Dissociation area: 156.64 Å2
Dissociation energy (ΔGdiss): -2.7 kcal/mol
Dissociation entropy (TΔSdiss): 2.29 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-160015
Monomeric assembly 2 of PDB entry 3v8v coloured by chemically distinct molecules, front view.
Monomeric assembly 2 of PDB entry 3v8v coloured by chemically distinct molecules, side view.
Monomeric assembly 2 of PDB entry 3v8v coloured by chemically distinct molecules, top view.
    Assembly 2
Confidence : 95%
No. subunits : 1
Symmetry : None
More details
3DComplex & QSbio predictionx
No. subunits : 1
Symmetry : None
Evidence : This biological assembly agrees with the prediction of both PISA & EPPIC

Macromolecules

Ribosomal RNA large subunit methyltransferase K/L
Chains: A, B
Length: 702 amino acids
Theoretical weight: 78.96 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P75864 (Residues: 1-702; Coverage: 100%)
Gene names: JW0931, b0948, rlmK, rlmKL, rlmL, ycbY
Pfam:
InterPro:
CATH:
Ribosomal RNA large subunit methyltransferase K/L in PDB entry 3v8v, assembly 1, front view.
Ribosomal RNA large subunit methyltransferase K/L in PDB entry 3v8v, assembly 1, side view.
Ribosomal RNA large subunit methyltransferase K/L in PDB entry 3v8v, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P75864  
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