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Figure 1.
Fig. 1. Residues in the cofactor TDP binding fold of
human BCKD. The inverted V-shaped conformation of cofactor TDP
is stabilized by stacking of the aminopyrimidine ring against
the side chain of Tyr-102-  ' from the
' subunit
(in greenish yellow) and the side chain of Leu-164-  from the
subunit
(in magenta). The invariant Glu-76- ' important
for cofactor activation coordinates to the N-1' atom of the
aminopyrimidine ring (3.4 Å apart). A ketoacid substrate
analog (in gray) labeled isocaproate is covalently modeled into
the side chain of His-146- ', based on
the crystal structure of BCKD from Pseudomonas putida (6). The
carboxylate group of the inhibitor interacts with the N-4' amino
group of TDP (separated by a distance of 4.3 Å). The side
chain of Ser-162- also
coordinates to the N-4' amino group (3.0 Å apart) to
position the cofactor in the correct conformation. Residue
Ser-292- is
phosphorylation site 1 of human BCKD. The diphosphate moiety of
TDP is stabilized, in part, by an octahedral coordination of the
Mg2+ ion. Two of the amino acid ligands Glu-193- and
Asn-222- in this
coordination are shown. Side chains of Arg-114- , Arg-220-
, and
His-291- , are, in
turn, in direct contact with the distal phosphate oxygens,
whereas the side chains of Gln-112- and
Tyr-113- (not shown)
interact with the proximal phosphate oxygens of the diphosphate
moiety of TDP.
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