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PDBsum entry 2rd5
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Protein binding
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PDB id
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2rd5
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References listed in PDB file
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Key reference
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Title
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Structural basis for the regulation of n-Acetylglutamate kinase by pii in arabidopsis thaliana.
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Authors
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Y.Mizuno,
G.B.Moorhead,
K.K.Ng.
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Ref.
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J Biol Chem, 2007,
282,
35733-35740.
[DOI no: ]
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PubMed id
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Abstract
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PII is a highly conserved regulatory protein found in organisms across the three
domains of life. In cyanobacteria and plants, PII relieves the feedback
inhibition of the rate-limiting step in arginine biosynthesis catalyzed by
N-acetylglutamate kinase (NAGK). To understand the molecular structural basis of
enzyme regulation by PII, we have determined a 2.5-A resolution crystal
structure of a complex formed between two homotrimers of PII and a single
hexamer of NAGK from Arabidopsis thaliana bound to the metabolites
N-acetylglutamate, ADP, ATP, and arginine. In PII, the T-loop and Trp(22) at the
start of the alpha1-helix, which are both adjacent to the ATP-binding site of
PII, contact two beta-strands as well as the ends of two central helices (alphaE
and alphaG) in NAGK, the opposing ends of which form major portions of the ATP
and N-acetylglutamate substrate-binding sites. The binding of Mg(2+).ATP to PII
stabilizes a conformation of the T-loop that favors interactions with both open
and closed conformations of NAGK. Interactions between PII and NAGK appear to
limit the degree of opening and closing of the active-site cleft in opposition
to a domain-separating inhibitory effect exerted by arginine, thus explaining
the stimulatory effect of PII on the kinetics of arginine-inhibited NAGK.
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Figure 1.
Overall structure of the PII·NAGK complex.A and B, top
and bottom views, respectively, along the molecular 3-fold
rotational axis; C, side view along the 2-fold axis bisecting
interface A; D, side view along the 2-fold axis bisecting
interface B. In A and B, the views taken in C and D are marked
with gray letters beside the respective 2-fold rotational axes.
In C and D, the views taken in A and B are marked with gray
letters beside the 3-fold rotational axis. PII is colored dark
gray; ATP bound to PII and ADP bound to NAGK are colored
magenta. NAGK protomers are colored yellow and green;
N-acetylglutamate (NAG) is colored red, and arginine is colored
blue. Figs. 1, 2, 3, 4 were prepared using PyMOL (38).
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Figure 4.
Open and closed conformations of NAGK drawn as α-carbon
traces. Shown are the open (A) and closed (B) conformations of
A. thaliana NAGK and the open conformation of T. maritima NAGK
bound to arginine (C) (21). ADP and N-acetylglutamate (NAG) are
drawn in stick representation. The N-terminal domain (N-term;
residues 15-211) is colored blue, and the C-terminal domain
(C-term; residues 212-297) is colored red. The black dot marks
the position of the rotational axis that is normal to the plane
of the page. Rotating the N-terminal domain of the open form of
NAGK by 11° about this axis in the direction indicated by
the arrow in A would result in the closed conformation shown in
B. The right panels show a “top” view similar to that used
in Fig. 2A. This view is perpendicular to the rotational axis,
which is drawn as a light gray arrow.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
35733-35740)
copyright 2007.
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