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PDBsum entry 1xfy
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Lyase/metal binding protein
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PDB id
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1xfy
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Contents |
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(+ 0 more)
735 a.a.
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(+ 0 more)
146 a.a.
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References listed in PDB file
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Key reference
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Title
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Calcium-Independent calmodulin binding and two-Metal-Ion catalytic mechanism of anthrax edema factor.
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Authors
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Y.Shen,
N.L.Zhukovskaya,
Q.Guo,
J.Florián,
W.J.Tang.
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Ref.
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EMBO J, 2005,
24,
929-941.
[DOI no: ]
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PubMed id
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Abstract
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Edema factor (EF), a key anthrax exotoxin, has an anthrax protective
antigen-binding domain (PABD) and a calmodulin (CaM)-activated adenylyl cyclase
domain. Here, we report the crystal structures of CaM-bound EF, revealing the
architecture of EF PABD. CaM has N- and C-terminal domains and each domain can
bind two calcium ions. Calcium binding induces the conformational change of CaM
from closed to open. Structures of the EF-CaM complex show how EF locks the
N-terminal domain of CaM into a closed conformation regardless of its
calcium-loading state. This represents a mechanism of how CaM effector alters
the calcium affinity of CaM and uncouples the conformational change of CaM from
calcium loading. Furthermore, structures of EF-CaM complexed with nucleotides
show that EF uses two-metal-ion catalysis, a prevalent mechanism in DNA and RNA
polymerases. A histidine (H351) further facilitates the catalysis of EF by
activating a water to deprotonate 3'OH of ATP. Mammalian adenylyl cyclases share
no structural similarity with EF and they also use two-metal-ion catalysis,
suggesting the catalytic mechanism-driven convergent evolution of two
structurally diverse adenylyl cyclases.
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Figure 1.
Figure 1 Structure of EF -CaM complex. (A) Ribbon diagram of EF
in complex with CaM and that of LF. Catalytic core domain,
helical domain, N-terminal PABD, and C-terminal PABD of EF are
colored in green, yellow, blue, and purple, respectively, and
CaM in red. N-terminal PABD, C-terminal PABD, and protease
domain of LF are in blue, purple and green, respectively. (B)
Comparison of PABDs of EF and LF. The similar secondary
structures of the N-terminal  /
 sandwich
of PABDs of EF and LF are depicted in blue and dark blue,
respectively, and those of the C-terminal five-helix domain of
PABD of EF and LF are colored in purple and magenta,
respectively. Five loops, L1 -L5, which have significant
differences between EF-PABD and LF-PABD, are colored in cyan and
yellow, respectively. (C) Sequence alignment of PABD of EF and
LF. Identical sequences are colored in yellow and similar
sequences are in green.
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Figure 2.
Figure 2 Structures of N-CaM and its interaction with EF. (A)
Structures of N-CaM (red) in EF -CaM complex at 1  M
calcium, 1 mM calcium, 10 mM calcium concentrations in
comparison with the calcium-free N-CaM structure (left, PDB
code: 1CFD) and the crystal structure of four calcium-loaded CaM
(right, PDB code: 1CLL). Calcium ions are colored in orange. (B)
The interaction between N-CaM and the helical domain of EF. The
helical domains of EF and N-CaM of the EF -CaM complex at 10 mM
calcium concentration are colored in yellow and red,
respectively. For comparison, four calcium-loaded CaM is shown
in cyan. (C) Detailed hydrogen bonding and salt bridge formed at
the interface between helices I and II of N-CaM and helices L
and M of EF.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2005,
24,
929-941)
copyright 2005.
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