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PDBsum entry 1dy1
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Angiogenesis inhibitor
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PDB id
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1dy1
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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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Variable zinc coordination in endostatin.
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Authors
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E.Hohenester,
T.Sasaki,
K.Mann,
R.Timpl.
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Ref.
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J Mol Biol, 2000,
297,
1-6.
[DOI no: ]
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PubMed id
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Abstract
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Endostatin is a proteolytic fragment of collagen XVIII that potently inhibits
angiogenesis and tumour growth. Human endostatin contains a zinc ion, bound near
the N terminus, which was not observed in the original structure of mouse
endostatin at pH 5. Controversial data exist on the role of this zinc ion in the
anti-tumour activity. We report two new crystal structures of mouse endostatin
at pH 8.5 with bound zinc. One crystal form shows a metal ion coordination
similar to that in human endostatin (His132, His134, His142, Asp207), but the
conformation of the N-terminal segment is different. In the other crystal form,
Asp136 replaces His132 as a zinc ligand. Site-directed mutagenesis of
zinc-binding residues demonstrates that both coordination geometries occur in
solution. The large degree of structural heterogeneity of the zinc-binding site
has implications for endostatin function. We conclude that zinc is likely to
play a structural rather than a critical functional role in endostatin.
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Figure 1.
Figure 1. (2F[obs] -F[calc]), a[calc] simulated annealing
omit maps of the region around the zinc-binding site in (a)
mouse endostatin crystal form II and (b) crystal form III.
Residues up to His142 and the zinc ion were excluded from the
phasing model. The final refined models are shown superimposed
on the maps. The zinc ion is shown as a pink sphere. Residues
coordinating to the zinc ion have been labelled and metal-ligand
bonds are shown as black sticks. Made with BOBSCRIPT (Kraulis
1991 and Esnouf 1997) and Raster3D (Merrit & Murphy, 1994).
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Figure 2.
Figure 2. (a) Alignment of the N-terminal sequences of
mouse and human endostatin. Residues added by the cloning
process are in grey. Zinc-binding residues are marked by filled
circles. (b) Comparison of the crystal structures of mouse
endostatin forms II and III (in blue and green, respectively)
and human endostatin (Ding et al., 1998; in pink). The
structures were superimposed on residues 142-310 (mouse
numbering scheme; Hohenester et al., 1998). The zinc ions are
shown as spheres. The side-chains of His132, His134, and Asp136
are shown for all three structures; the side-chains of His142
and Asp207 are in almost identical positions in the three
structures (see the text) and are shown only for mouse
endostatin form II. Made with BOBSCRIPT (Kraulis 1991 and Esnouf
1997) and Raster3D (Merrit & Murphy, 1994).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
297,
1-6)
copyright 2000.
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Secondary reference #1
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Title
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Crystal structure of the angiogenesis inhibitor endostatin at 1.5 a resolution.
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Authors
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E.Hohenester,
T.Sasaki,
B.R.Olsen,
R.Timpl.
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Ref.
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EMBO J, 1998,
17,
1656-1664.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Stereo view of the final 2F[obs]-F[calc] map at 1.5 Å
resolution. The region around  -strand
P is shown, with the disulphide bond between Cys164 and Cys304
in the centre. The map is contoured at the 1.5  level
and is shown with the refined model superimposed. The figure was
made with BOBSCRIPT (R.Esnouf, personal communication), a
modified version of MOLSCRIPT (Kraulis, 1991).
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Figure 5.
Figure 5 Electrostatic surface representation (Nicholls, 1992)
of endostatin. The two views of the endostatin surface are
related by a rotation of 130° about the horizontal axis. Blue
indicates regions of positive potential and red regions of
negative potential, at the 5 kT/e level. The N- and the
C-termini are indicated; basic residues and the solvent-exposed
side chains of Phe162 and Phe165 are labelled in yellow and
white, respectively. The hatched area corresponds to the
oligosaccharide-binding site of C-type lectin CRDs.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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