Figure 1.
Figure 1: Crystal structure of the anaerobic Michaelis complex
of E. coli AlkB- Delta-N11
with Fe(ii), 2OG and a methylated trinucleotide. a, Stereo
ribbon diagram with the backbone coloured and the 2° structural
elements labelled according to subdomain organization (with the
N-terminal extension (N) in yellow, nucleotide-recognition lid
(L) in blue, and catalytic core (C) in green as in the
sequence-structure alignment in Supplementary Fig. S2A). Most of
the blue segment is protected against amide H/D exchange by
dT-(1-me-dA)-dT substrate binding (Supplementary Fig. S2A). The
sphere representing the Fe cofactor is coloured orange, whereas
atoms in 2OG and dT-(1-me-dA)-dT are coloured according to
atomic identity (carbon, white; oxygen, red; nitrogen, blue; and
phosphorous, orange). Invariant side chains in Fe-2OG
dioxygenases are coloured red or magenta depending on whether
they interact with Fe or 2OG, respectively. b, Least-squares
superposition of 80 out of 211 C atoms
in AlkB with a root mean square deviation of 2.1 Å with the
equivalent atoms in the taurine oxidase TauD^16 (Protein Data
Bank 1OS7; protein backbone and ligands coloured red). In TauD,
the 1-carboxylate of 2OG interacts with Fe in the alternative
geometry observed in crystal structures of some Fe-2OG
dioxygenases before O[2]-analogue binding18.
N11
with Fe(ii), 2OG and a methylated trinucleotide. a, Stereo
ribbon diagram with the backbone coloured and the 2° structural
elements labelled according to subdomain organization (with the
N-terminal extension (N) in yellow, nucleotide-recognition lid
(L) in blue, and catalytic core (C) in green as in the
sequence-structure alignment in Supplementary Fig. S2A). Most of
the blue segment is protected against amide H/D exchange by
dT-(1-me-dA)-dT substrate binding (Supplementary Fig. S2A). The
sphere representing the Fe cofactor is coloured orange, whereas
atoms in 2OG and dT-(1-me-dA)-dT are coloured according to
atomic identity (carbon, white; oxygen, red; nitrogen, blue; and
phosphorous, orange). Invariant side chains in Fe-2OG
dioxygenases are coloured red or magenta depending on whether
they interact with Fe or 2OG, respectively. b, Least-squares
superposition of 80 out of 211 C 
atoms
in AlkB with a root mean square deviation of 2.1 Å with the
equivalent atoms in the taurine oxidase TauD^16 (Protein Data
Bank 1OS7; protein backbone and ligands coloured red). In TauD,
the 1-carboxylate of 2OG interacts with Fe in the alternative
geometry observed in crystal structures of some Fe-2OG
dioxygenases before O[2]-analogue binding18.