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PDBsum entry 1eeh
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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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&Quot;open" structures of murd: domain movements and structural similarities with folylpolyglutamate synthetase.
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Authors
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J.A.Bertrand,
E.Fanchon,
L.Martin,
L.Chantalat,
G.Auger,
D.Blanot,
J.Van heijenoort,
O.Dideberg.
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Ref.
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J Mol Biol, 2000,
301,
1257-1266.
[DOI no: ]
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PubMed id
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Abstract
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UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase catalyses the addition
of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine (UMA).
The crystal structures of Escherichia coli in the substrate-free form and MurD
complexed with UMA have been determined at 2.4 A and 1.88 A resolution,
respectively. The MurD structure comprises three domains each of a topology
reminiscent of nucleotide-binding folds. In the two structures the C-terminal
domain undergoes a large rigid-body rotation away from the N-terminal and
central domains. These two "open" structures were compared with the
four published "closed" structures of MurD. In addition the comparison
reveals which regions are affected by the binding of UMA, ATP and d-Glu. Also we
compare and discuss two structurally characterized enzymes which belong to the
same ligase superfamily: MurD and folylpolyglutamate synthetase (FGS). The
analysis allows the identification of key residues involved in the reaction
mechanism of FGS. The determination of the two "open" conformation
structures represents a new step towards the complete elucidation of the
enzymatic mechanism of the MurD ligase.
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Figure 5.
Figure 5. Stereo view showing the "closed" form model of
FGS (black) superimposed on the central and C-terminal domains
of MurD.UMA.ADP.Mg2+ (green). The Image -Ala of UMA is shown in
red and ADP in blue.
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Figure 6.
Figure 6. Stereo view of the active-site region of the
"closed" conformation of FGS. Residues that play a role in the
binding of either ADP.Mg2+ and/or the terminal carboxylate group
of UMA are labelled. The carboxylate group of UMA is shown in
orange, ADP in deep blue, water molecules in red and Mg2+ in
black. The blue lines show strand b6, the P-loop and the
beginning of helix a6.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
301,
1257-1266)
copyright 2000.
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Secondary reference #1
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Title
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Crystal structure of udp-N-Acetylmuramoyl-L-Alanine:d-Glutamate ligase from escherichia coli.
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Authors
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J.A.Bertrand,
G.Auger,
E.Fanchon,
L.Martin,
D.Blanot,
J.Van heijenoort,
O.Dideberg.
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Ref.
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Embo J, 1997,
16,
3416-3425.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Ribbon diagram of the binary complex of MurD and UMA
produced with the program Molscript (Kraulis, 1991). Domain 1 is
shown in pink, domain 2 in blue, domain 3 in green and UMA in
red. For reasons of continuity, the two missing loops in the
structure, residues 221 -225 and 241 -244, are shown
interconnected in the figure.
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Figure 6.
Figure 6 Proposed catalytic mechanism for the formation of
UDP-N-acetylmuramoyl-L-alanine-D-glutamate by MurD.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Determination of the murd mechanism through crystallographic analysis of enzyme complexes.
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Authors
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J.A.Bertrand,
G.Auger,
L.Martin,
E.Fanchon,
D.Blanot,
D.Le beller,
J.Van heijenoort,
O.Dideberg.
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Ref.
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J Mol Biol, 1999,
289,
579-590.
[DOI no: ]
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PubMed id
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Figure 6.
Figure 6. Stereo diagram show-
ing UMAG bound in the cleft
formed by the three domains. The
C
a
trace is shown in yellow, blue
and green for the N-terminal, cen-
tral and C-terminal domains,
respectively. Some sections of the
central domain C
a
trace were
clipped for the sake of clarity. Resi-
dues that interact with UMAG
though either hydrophobic or
hydrophilic interactions are shown.
In the Figure, Asn138 is located
behind UMAG and is unlabelled.
W1 is a structurally conserved
water molecule (Wat600).
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Figure 8.
Figure 8. Proposed reaction mechanism for the synthesis of UMAG by E. coli MurD. Only Mg
2+
and amino acid
side-chains involved in the mechanism are included.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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