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PDBsum entry 1s8h
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Hydrolase, toxin
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PDB id
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1s8h
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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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A molecular mechanism for lys49-Phospholipase a2 activity based on ligand-Induced conformational change.
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Authors
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A.L.Ambrosio,
M.C.Nonato,
H.S.De araújo,
R.Arni,
R.J.Ward,
C.L.Ownby,
D.H.De souza,
R.C.Garratt.
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Ref.
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J Biol Chem, 2005,
280,
7326-7335.
[DOI no: ]
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PubMed id
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Abstract
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Agkistrodon contortrix laticinctus myotoxin is a Lys(49)-phospholipase A(2) (EC
3.1.1.4) isolated from the venom of the serpent A. contortrix laticinctus
(broad-banded copperhead). We present here three monomeric crystal structures of
the myotoxin, obtained under different crystallization conditions. The three
forms present notable structural differences and reveal that the presence of a
ligand in the active site (naturally presumed to be a fatty acid) induces the
exposure of a hydrophobic surface (the hydrophobic knuckle) toward the C
terminus. The knuckle in A. contortrix laticinctus myotoxin involves the side
chains of Phe(121) and Phe(124) and is a consequence of the formation of a
canonical structure for the main chain within the region of residues 118-125.
Comparison with other Lys(49)-phospholipase A(2) myotoxins shows that although
the knuckle is a generic structural motif common to all members of the family,
it is not readily recognizable by simple sequence analyses. An activation
mechanism is proposed that relates fatty acid retention at the active site to
conformational changes within the C-terminal region, a part of the molecule that
has long been associated with Ca(2+)-independent membrane damaging activity and
myotoxicity. This provides, for the first time, a direct structural connection
between the phospholipase "active site" and the C-terminal
"myotoxic site," justifying the otherwise enigmatic conservation of
the residues of the former in supposedly catalytically inactive molecules.
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Figure 4.
FIG. 4. Stereo view ribbon representation of the C terminus
and calcium binding loops of the 18 available structures.
Thirteen of the 18 available structures of Lys49-PLA[2] present
the canonical conformation. Red, form I of ACL myotoxin (PDB
code 1S8G [PDB]
), chains A and B of piratoxin-II (PDB code 1QLL [PDB]
), chains A and B of myotoxin-II (PDB code 1CLP [PDB]
), chain A of structure 1, and chains A and B of structure 2, a
monomer of structure 3 (with stearic acid bound), where a slight
difference in the conformation of residues Tyr120 and Leu121 is
observed, and monomer of structure 4 (complexed with a PEG
fragment) of BthTX-I, acutohemolysin (PDB code 1MC2 [PDB]
), and chains A and B for NumMT-I, both in complex with stearic
acid. The Lys122 (C-  shown as balls)
interacts with the Cys29-Gly30 peptide bond at the Ca^2+ binding
loop. Moreover, seven of these present a fatty acid molecule
inside the hydrophobic channel. The remaining five structures
where the Lys122 points toward the solvent region and the C
terminus show a high degree of variability: in white, form II of
ACL myotoxin (PDB code 1S8H [PDB]
) and A. piscivorus piscivorus (PDB code 1PPA [PDB]
); in yellow, chain B of structure I from BthTX-I; in green,
form III of ACL myotoxin (PDB code 1S8I [PDB]
), and in blue, GodMT-II (1GOD).
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Figure 6.
FIG. 6. The hydrophobic knuckle. a, presence of a large
non-polar surface exposed to the solvent (potential surface map,
calculated by GRASP (89)), formed by hydrophobic residues
surrounding Lys122, and constituting the hydrophobic knuckle. In
all cases, Lys122 interacts with the Cys29-Gly30 peptide bond,
and a ligand is bound to the hydrophobic channel. Positive
charges surround the base of the knuckle. b, the knuckle can
also be observed in ligand-free structures that present the
canonical conformation for the C-terminal region, where Lys122
interacts with Cys29-Gly30 peptide bond. c, structures where
Lys122 is exposed to the solvent, the hydrophobic knuckle is not
observed.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
7326-7335)
copyright 2005.
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