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Structure paper

TitleRibosomal oxygenases are structurally conserved from prokaryotes to humans.
Journal, issue, pagesNature, Vol. 510, Page 422-426, Year 2014
Publish dateMay 7, 2010 (structure data deposition date)
AuthorsChowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. ...Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J.
External linksNature / PubMed:24814345
MethodsX-ray diffraction
Resolution2.05 - 2.96 Å
Structure data

PDB-2xdv:
Crystal Structure of the Catalytic Domain of FLJ14393
Method: X-RAY DIFFRACTION / Resolution: 2.57 Å

PDB-4bu2:
60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and 2-oxoglutarate (2OG)
Method: X-RAY DIFFRACTION / Resolution: 2.78 Å

PDB-4bxf:
60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-4ccj:
60S ribosomal protein L8 histidine hydroxylase (NO66) in apo form
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-4cck:
60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and N-oxalylglycine (NOG)
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-4ccl:
X-Ray structure of E. coli ycfD
Method: X-RAY DIFFRACTION / Resolution: 2.596 Å

PDB-4ccm:
60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1)
Method: X-RAY DIFFRACTION / Resolution: 2.51 Å

PDB-4ccn:
60S ribosomal protein L8 histidine hydroxylase (NO66 L299C/C300S) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-2)
Method: X-RAY DIFFRACTION / Resolution: 2.23 Å

PDB-4cco:
60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-4csw:
Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase
Method: X-RAY DIFFRACTION / Resolution: 2.821 Å

PDB-4cug:
Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase in complex substrate fragment
Method: X-RAY DIFFRACTION / Resolution: 2.96 Å

PDB-4lit:
Structure of YcfD a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and 2-oxoglutarate.
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-4liu:
Structure of YcfD, a Ribosomal oxygenase from Escherichia coli.
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-4liv:
Structure of YcfD, a Ribosomal oxygenase from Escherichia coli in complex with Cobalt and succinic acid.
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-OGA:
N-OXALYLGLYCINE / inhibitor*YM / N-Oxalylglycine

ChemComp-NI:
NICKEL (II) ION / Nickel

ChemComp-MN:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-CD:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-AKG:
2-OXOGLUTARIC ACID / Α-Ketoglutaric acid

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-CIT:
CITRIC ACID / Citric acid

ChemComp-UN9:
N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM / 2-Methyl-2,4-pentanediol

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-CO:
Unknown entry

ChemComp-TAM:
TRIS(HYDROXYETHYL)AMINOMETHANE / pH buffer*YM / Tris

ChemComp-SIN:
SUCCINIC ACID / Succinic acid

Source
  • homo sapiens (human)
  • escherichia coli (E. coli)
  • rhodothermus marinus (bacteria)
KeywordsNUCLEAR PROTEIN / RIBOSOME BIOGENESIS / OXIDOREDUCTASE / NON-HEME / IRON-BINDING / DSBH / 2-OXOGLUTARATE / DIOXYGENASE / JMJC DOMAIN / RPL27A / BETA-HYDROXYLATION / TRANSCRIPTION AND EPIGENETIC REGULATION / SIGNALING / OXIDOREDUCTASE/TRANSLATION / OXIDOREDUCTASE-TRANSLATION COMPLEX / RPL8 / 2OG AND IRON DEPENDENT OXYGENASE / 2- OXOGLUTARATE / 2-OXOGLUTARATE AND IRON DEPENDENT OXYGENASE / DOUBLE STRANDED BETA HELIX FOLD / TRANSLATION / Hydroxylation

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