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PDBsum entry 2dw2
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Apoptosis, toxin
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PDB id
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2dw2
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References listed in PDB file
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Key reference
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Title
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Crystal structures of catrocollastatin/vap2b reveal a dynamic, Modular architecture of adam/adamalysin/reprolysin family proteins.
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Authors
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T.Igarashi,
S.Araki,
H.Mori,
S.Takeda.
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Ref.
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Febs Lett, 2007,
581,
2416-2422.
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PubMed id
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Abstract
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Catrocollastatin/vascular apoptosis-inducing protein (VAP)2B is a
metalloproteinase from Crotalus atrox venom, possessing
metalloproteinase/disintegrin/cysteine-rich (MDC) domains that bear the typical
domain architecture of a disintegrin and metalloproteinase
(ADAM)/adamalysin/reprolysin family proteins. Here we describe crystal
structures of catrocollastatin/VAP2B in three different crystal forms,
representing the first reported crystal structures of a member of the monomeric
class of this family of proteins. The overall structures show good agreement
with both monomers of atypical homodimeric VAP1. Comparison of the six
catrocollastatin/VAP2B monomer structures and the structures of VAP1 reveals a
dynamic, modular architecture that may be important for the functions of
ADAM/adamalysin/reprolysin family proteins.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray crystallographic analysis of two vascular apoptosis-Inducing proteins (vaps) from crotalus atrox venom.
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Authors
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T.Igarashi,
Y.Oishi,
S.Araki,
H.Mori,
S.Takeda.
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Ref.
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Acta Crystallograph Sect F Struct Biol Cryst Commun, 2006,
62,
688-691.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 VAP2 crystals. (a) Form 2-2, (b) form 2-3, (c) form
2-4 and (d) form 2-5 crystals. The scale bars indicate 0.1 mm.
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The above figure is
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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Secondary reference #2
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Title
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Crystal structures of vap1 reveal adams' Mdc domain architecture and its unique c-Shaped scaffold.
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Authors
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S.Takeda,
T.Igarashi,
H.Mori,
S.Araki.
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Ref.
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EMBO J, 2006,
25,
2388-2396.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 MDC architecture. (A) VAP1 dimer viewed from the NCS
axis. The H0-helix, M-domain, linker, D[s]-, D[a]-, C[w]-, and
C[h]-domains and HVRs belonging to the one monomer are shown in
red, yellow, gray, cyan, pink, gray, green and blue,
respectively. The disulfide-linked counterpart is shown in gray.
Zinc and calcium ions are represented as red and black spheres,
respectively. The NAG (N-acetyl-glucosamine, in orange) moieties
linked to Asn218, the calcium-mimetic Lys202 and the bound
inhibitor GM6001 (GM, in green) are in ball-stick
representations. (B) Stereo view of VAP1 monomer from the
direction nearly perpendicular to (A). The helix numbers are
labelled. (C) Superposition of the M-domains of ADAM33 (blue)
and VAP1 (yellow). The calcium ion bound to site I and the zinc
ion in ADAM33 are represented by black and red spheres,
respectively. The disulfide bridges are indicated in black and
blue letters for VAP1 and ADAM33, respectively. The QDHSK
sequence for the dimer interface in VAP1 (residues 320–324) is
in red. (D) Comparison of the calcium-binding site I structures
of ADAM33 (blue) and VAP1 (yellow) in stereo. The residues in
ADAM33 and in VAP1 are labelled in blue and black, respectively.
A calcium ion and a water molecule bound to ADAM33 are
represented as green and red spheres, respectively. The ammonium
group of Lys202 in VAP1 occupies the position of the calcium ion
in ADAM33. In ADAM33 (Orth et al, 2004), side-chain oxygen atoms
of Glu213, Asp296 and Asn407, the carbonyl oxygen of Cys404 and
a water molecule form the corners of a pentagonal bipyramid and
ligand to the calcium ion.
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Figure 4.
Figure 4 C-domain architecture and HVR. (A) The C-domain
architecture in stereo. The C[w]- and C[h]-domains are in gray
and light green, respectively. The disulfide bridges and the
residues forming the hydrophobic ridges are indicated. The HVR
and its NCS counterpart are shown in red and blue, respectively.
The variable loop (residues 539–549), flanked by two adjacent
cysteine residues, is in green. (B) Crystal packing in the
orthorhombic crystal. The crystallographically equivalent
molecules (HVRs) are in cyan (blue) and pink (red),
respectively. The arrows indicate the directions of the HVR
chains. Zinc and calcium ions are represented as red and black
spheres, respectively. (C) Interactions between the HVRs (cyan
and pink) in stereo. The molecular surface of the cyan molecule
is shown with the electrochemical surface potential (red to
blue). The residues constituting the hydrophobic ridges are in
yellow. The residues are labelled in blue and red for cyan and
pink, respectively. (D) Water-mediated hydrogen-bond network in
the HVR. The HVR residues are in pink and cyan; non-HVR residues
in the pink molecule are in gray.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #3
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Title
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Cdna cloning and some additional peptide characterization of a single-Chain vascular apoptosis-Inducing protein, Vap2.
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Authors
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S.Masuda,
H.Maeda,
J.Y.Miao,
H.Hayashi,
S.Araki.
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Ref.
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Endothelium, 2007,
14,
89-96.
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PubMed id
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Secondary reference #4
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Title
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Two vascular apoptosis-Inducing proteins from snake venom are members of the metalloprotease/disintegrin family.
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Authors
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S.Masuda,
H.Hayashi,
S.Araki.
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Ref.
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Eur J Biochem, 1998,
253,
36-41.
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PubMed id
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