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PDBsum entry 2evr
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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 of murein peptide specificity of a gamma-D-Glutamyl-L-Diamino acid endopeptidase.
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Authors
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Q.Xu,
S.Sudek,
D.Mcmullan,
M.D.Miller,
B.Geierstanger,
D.H.Jones,
S.S.Krishna,
G.Spraggon,
B.Bursalay,
P.Abdubek,
C.Acosta,
E.Ambing,
T.Astakhova,
H.L.Axelrod,
D.Carlton,
J.Caruthers,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
Y.Elias,
M.A.Elsliger,
J.Feuerhelm,
S.K.Grzechnik,
J.Hale,
G.Won han,
J.Haugen,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
A.Kumar,
D.Marciano,
A.T.Morse,
E.Nigoghossian,
L.Okach,
S.Oommachen,
J.Paulsen,
R.Reyes,
C.L.Rife,
C.V.Trout,
H.Van den bedem,
D.Weekes,
A.White,
G.Wolf,
C.Zubieta,
K.O.Hodgson,
J.Wooley,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
I.A.Wilson.
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Ref.
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Structure, 2009,
17,
303-313.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of two homologous endopeptidases from cyanobacteria
Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 A
resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a
ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain.
The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of
cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved
catalytic core. We deduced from structure and sequence analysis, and then
experimentally, that these two proteins act as gamma-D-glutamyl-L-diamino acid
endopeptidases (EC 3.4.22.-). The active site is located near the interface
between the SH3b and NlpC/P60 domains, where the SH3b domain may help define
substrate specificity, instead of functioning as a targeting domain, so that
only muropeptides with an N-terminal L-alanine can bind to the active site.
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Figure 3.
Figure 3. Bacterial SH3b Domains
Structural comparison
between the SH3b domain of AvPCP, ALE-1-targeting domain (PDB ID
code 1r77), GW3 domain (PDB ID code 1m9s; residue range
551–629) of invasion protein InlB, and Abl SH3 domain (PDB ID
code 1bbz). The four structures are shown in the same
superimposed orientation. Residues of the ALE-1-targeting
domain, the GW3 domain, and the Abl SH3 domain that can be
superimposed with AvPCP SH3b are colored red.
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Figure 4.
Figure 4. Structural Comparisons of the Catalytic Domain of
AvPCP
(A) Structural superimposition of the catalytic
domains of AvPCP (green) and papain (PDB ID code 9pap; orange)
in stereo. The catalytic triad of each protein is shown as
sticks.
(B) Comparison of AvPCP with representative
papain-like proteins: papain, Spr, the CHAP domain of GspS
(Gsps-N), 2p1g (PDB ID code 2p1g), and NsPCS (PDB ID code 2bu3).
The structures are shown in the same orientation of their
catalytic domains.
(C) Four representative active-site
pockets. The cysteine in the catalytic triad is colored in red,
the histidine in blue, and the third polar residue in cyan (seen
only in 2p1g, buried in others). The S sites (labeled S) are
tentatively assigned based on papain.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2009,
17,
303-313)
copyright 2009.
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