PDBsum entry 1dy1

Angiogenesis inhibitor

PDB id: 1dy1

Contents

Protein chain

183 a.a. *

Metals

_ZN ×2

Waters ×47

* Residue conservation analysis

PDB id:

1dy1

Name:

Angiogenesis inhibitor

Title:

Murine endostatin, crystal form iii

Structure:

Collagen alpha1(xviii) chain. Chain: a. Fragment: endostatin domain. Engineered: yes. Mutation: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: ebna-293. Expression_system_cell: embryonic kidney cell.

Resolution:

2.20Å R-factor: 0.195 R-free: 0.270

Authors:

E.Hohenester,T.Sasaki,R.Timpl

Key ref:

E.Hohenester et al. (2000). Variable zinc coordination in endostatin. J Mol Biol, 297, 1-6. PubMed id: 10704302 DOI: 10.1006/jmbi.2000.3553

Date:

21-Jan-00 Release date: 21-Jan-01

Protein chain

P39061  (COIA1_MOUSE) -  Collagen alpha-1(XVIII) chain from Mus musculus

Seq: 1774 a.a.

Struc: 183 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1006/jmbi.2000.3553

J Mol Biol 297:1-6 (2000)

PubMed id: 10704302

Variable zinc coordination in endostatin.

E.Hohenester, T.Sasaki, K.Mann, R.Timpl.

ABSTRACT

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.

Selected figure(s)

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).

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).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 1-6) copyright 2000.