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PDBsum entry 1ee1
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Stabilization of active-Site loops in nh3-Dependent NAD+ synthetase from bacillus subtilis.
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Authors
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Y.Devedjiev,
J.Symersky,
R.Singh,
M.Jedrzejas,
C.Brouillette,
W.Brouillette,
D.Muccio,
D.Chattopadhyay,
L.Delucas.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
806-812.
[DOI no: ]
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PubMed id
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Abstract
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The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of
nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid
adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active
site, including stabilization of flexible loops 82-87 and 204-225, has been
studied by determination of the crystal structures of complexes of NADS with
natural substrates and a substrate analog. Both loops are stabilized
independently of NaAD and solely from the ATP-binding site. Analysis of the
binding contacts suggests that the minor loop 82-87 is stabilized primarily by a
hydrogen bond with the adenine base of ATP. Formation of a coordination complex
with Mg(2+) in the ATP-binding site may contribute to the stabilization of the
major loop 204-225. The major loop has a role in substrate recognition and
stabilization, in addition to the protection of the reaction intermediate
described previously. A second and novel Mg(2+) position has been observed
closer to the NaAD-binding site in the structure crystallized at pH 7.5, where
the enzyme is active. This could therefore be the catalytically active Mg(2+).
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Figure 1.
Figure 1 A scheme of the reaction catalyzed by NAD^+ synthetase.
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Figure 6.
Figure 6 Coordination of Mg2+ in the ATP-binding site of NAD^+
synthetase. The nicotinosyl moiety of NaAD is shown in violet,
AMP in gold and PP[i] in red; Mg2+ with coordinated O atoms are
shown in silver, relevant amino-acid residues are in green and
the loop 204-225 is indicated by thin brown lines. Positions
Mg(I), Mg(II) and Mg(III) are explained in the text.
Coordination of the new Mg(III) position is indicated by thin
silver lines. The new conformation of Glu162 at pH 7.5 is shown
in cyan. ATP and AMP-CPP are not shown for clarity. Prepared
with RIBBONS (Carson, 1997[Carson, M. (1997). Methods Enzymol.
277, 493-505.]).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
806-812)
copyright 2001.
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Secondary reference #1
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Title
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Asymmetric complex of NAD+ synthetase with natural substrates ATP deamido-Nad+
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Authors
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Y.Devedjiev,
R.Singh,
C.Brouillette,
D.Muccio,
W.Brouillette,
L.Delucas,
M.Jedzejas.
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Ref.
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am cryst assoc , ...
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Secondary reference #2
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Title
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Catalytic cycle of NAD+ synthetase viewed by X-Ray structures of kinetic intermediates
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Authors
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Y.Devedjiev,
R.Singh,
C.Brouillette,
D.Muccio,
W.Brouillette,
L.Delucas,
M.Jedzejas.
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Ref.
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am cryst assoc , ...
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