 |
PDBsum entry 3n30
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Metal binding protein
|
PDB id
|
|
|
|
3n30
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Metal binding protein
|
|
|
Title:
|
|
Crystal structure of cubic zn3-hub (human ubiquitin) adduct
|
|
Structure:
|
|
Ubiquitin. Chain: a, b. Engineered: yes
|
|
Source:
|
|
Homo sapiens. Human. Organism_taxid: 9606. Gene: rps27a, uba80, ubcep1, uba52, ubcep2, ubb, ubc. Expressed in: escherichia coli. Expression_system_taxid: 562
|
|
Resolution:
|
|
|
3.00Å
|
R-factor:
|
0.238
|
R-free:
|
0.318
|
|
|
Authors:
|
|
D.Siliqi,R.Caliandro,F.Arnesano,G.Natile,G.Falini,S.Fermani, B.D.Belviso
|
|
Key ref:
|
|
F.Arnesano
et al.
(2011).
Crystallographic analysis of metal-ion binding to human ubiquitin.
Chemistry,
17,
1569-1578.
PubMed id:
|
|
|
Date:
|
|
|
19-May-10
|
Release date:
|
12-Jan-11
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P0CG48
(UBC_HUMAN) -
Polyubiquitin-C from Homo sapiens
|
|
|
|
Seq:
Struc:
|
|
|
|
685 a.a.
76 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Chemistry
17:1569-1578
(2011)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Crystallographic analysis of metal-ion binding to human ubiquitin.
|
|
F.Arnesano,
B.D.Belviso,
R.Caliandro,
G.Falini,
S.Fermani,
G.Natile,
D.Siliqi.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The metal-binding ability of human ubiquitin (hUb) towards a selection of
biologically relevant metal ions and complexes has been probed. Different
techniques have been used to obtain crystals suitable for crystallographic
analysis. In the first type of experiments, crystals of hUb have been soaked in
solutions containing copper(II) acetate and two metallodrugs, Zeise salt
(K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The
Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most
powerful anticancer drugs in clinical use. The Zeise salt readily reacts with
hUb crystals to afford an adduct with three platinum residues per protein
molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to
be unreactive for contact times up to one hour and to cause degradation of the
hUb crystals for longer times. In the second type of experiments, hUb was
cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin.
Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals
containing one metal ion per three molecules of protein, Zn-hUb(3) (already
reported in previous work), whereas at high metal-to-protein ratios (70:1) gives
crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In
contrast, once again, copper(II) acetate and cisplatin, even at low
metal-to-protein ratios, do not give crystalline material. In the soaking
experiment, the Zeise anion leads to simultaneous platination of His68, Met1,
and Lys6. Present and previous results of cocrystallization experiments
performed with Zn(II) and other Group 12 metal ions allow a comprehensive
understanding of the metal-ion binding properties of hUb with His68 as the main
anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64,
Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a
binding site. The amount of bound metal ion, with respect to that of the
protein, appears to be a relevant parameter influencing crystal packing.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Links
