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PDBsum entry 1kuf
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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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The 1.35 a structure of cadmium-Substituted tm-3, A snake-Venom metalloproteinase from taiwan habu: elucidation of a tnfalpha-Converting enzyme-Like active-Site structure with a distorted octahedral geometry of cadmium.
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Authors
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K.F.Huang,
S.H.Chiou,
T.P.Ko,
J.M.Yuann,
A.H.Wang.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2002,
58,
1118-1128.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of TM-3, a small snake-venom metalloproteinase (SVMP)
isolated from Taiwan habu (Trimeresurus mucrosquamatus), was determined at 1.35
A resolution with resultant R and R(free) values of 0.181 and 0.204,
respectively. The overall structure of TM-3 is an oblate ellipsoid that contains
three disulfide crosslinks, Cys118-Cys197, Cys159-Cys181 and Cys161-Cys164. It
exhibits the typical structural features of SVMPs and is closely related to the
structure of the catalytic proteinase domain of TNFalpha-converting enzyme
(TACE). In the present structure, the essential catalytic zinc ion was found to
be replaced by a cadmium ion during crystallization, as revealed by atomic
absorption analysis and X-ray data. This cadmium ion is bound to six ligands,
including three conserved histidines and three water molecules, displaying the
coordination geometry of a distorted octahedron. One of the water molecules is
proposed to play the role of stabilizing the tetrahedral intermediate during the
catalysis of SVMPs. The putative S'(1) specificity pocket of TM-3 is relatively
shallow, in contrast to the deep pockets of adamalysin II, atrolysin C and
H(2)-proteinase, but is similar to those in acutolysin A and TACE. The shallow
pocket is a consequence of the presence of the non-conserved disulfide bond
Cys159-Cys181 and the residue Gln174 at the bottom of the S'(1) pocket. The
results indicate that the active-site structure of TM-3, among the know
structures of SVMPs examined thus far, is most similar to that of TACE owing to
their close disulfide configurations and the S'(1) specificity pocket.
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Figure 2.
Figure 2 A ribbon diagram of the overall structure of TM-3. The
stereoview faces towards the active-site cleft. Cadmium ion and
its coordinated water molecules in the active site are depicted
as yellow and red spheres, respectively. The coordinated
histidines and catalytic glutamyl residue are denoted in blue by
a stick model. The three disulfide bridges are drawn in orange
as a ball-and-stick model. In addition, the locations of  -helices
(A-E),  -strands
(I-V) and the methionine-turn as well as the N- and C-terminal
residues are also indicated. The figure was produced using
MOLSCRIPT.
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Figure 4.
Figure 4 The active-site structure of TM-3. (a) A stereoview of
the 2F[o] - F[c] map (contoured at the 2.35  level)
of TM-3 around the active-site structure. Positions of various
residues in the active site are indicated and referred to those
in Fig. 2-. (b) Comparisons of the active-site structures of
TM-3, adamalysin II, acutolysin A and astacin. Zinc ions and
water molecules are shown as various spheres in green and
magenta, respectively. The Tyr149 in astacin is indicated as a
stick model in yellow. The figures were prepared using BOBSCRIPT
(a) and GRASP (b).
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2002,
58,
1118-1128)
copyright 2002.
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Secondary reference #1
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Title
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Characterization of multiple metalloproteinases with fibrinogenolytic activity from the venom of taiwan habu (trimeresurus mucrosquamatus): protein microsequencing coupled with cdna sequence analysis.
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Authors
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K.F.Huang,
C.C.Hung,
F.M.Pan,
L.P.Chow,
A.Tsugita,
S.H.Chiou.
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Ref.
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Biochem Biophys Res Commun, 1995,
216,
223-233.
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PubMed id
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