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PDBsum entry 1bzo
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Oxidoreductase
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PDB id
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1bzo
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Contents |
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* Residue conservation analysis
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PDB id:
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Oxidoreductase
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Title:
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Three-dimensional structure of prokaryotic cu,zn superoxide dismutase from p.Leiognathi, solved by x-ray crystallography.
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Structure:
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Protein (superoxide dismutase). Chain: a. Engineered: yes
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Source:
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Photobacterium leiognathi. Organism_taxid: 658. Cellular_location: periplasmic space. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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Dimer (from PDB file)
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Resolution:
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2.10Å
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R-factor:
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0.190
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R-free:
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0.260
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Authors:
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D.Bordo,D.Matak,K.Djinovic-Carugo,C.Rosano,A.Pesce,M.Bolognesi, M.E.Stroppolo,M.Falconi,A.Battistoni,A.Desideri
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Key ref:
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D.Bordo
et al.
(1999).
Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.
J Mol Biol,
285,
283-296.
PubMed id:
DOI:
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Date:
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02-Nov-98
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Release date:
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09-Apr-99
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PROCHECK
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Headers
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References
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P00446
(SODC_PHOLE) -
Superoxide dismutase [Cu-Zn] from Photobacterium leiognathi
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Seq:
Struc:
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173 a.a.
151 a.a.*
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Key: |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.1.15.1.1
- superoxide dismutase.
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Reaction:
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2 superoxide + 2 H+ = H2O2 + O2
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2
×
superoxide
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+
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2
×
H(+)
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=
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H2O2
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+
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O2
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Cofactor:
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Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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J Mol Biol
285:283-296
(1999)
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PubMed id:
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Evolutionary constraints for dimer formation in prokaryotic Cu,Zn superoxide dismutase.
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D.Bordo,
D.Matak,
K.Djinovic-Carugo,
C.Rosano,
A.Pesce,
M.Bolognesi,
M.E.Stroppolo,
M.Falconi,
A.Battistoni,
A.Desideri.
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ABSTRACT
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Prokaryotic Cu,Zn superoxide dismutases are characterized by a distinct
quaternary structure, as compared to that of the homologous eukaryotic enzymes.
Here we report a newly determined crystal structure of the dimeric Cu,Zn
superoxide dismutase from Photobacterium leiognathi (crystallized in space group
R32, refined at 2.5 A resolution, R-factor 0.19) and analyse it in comparison
with that of the monomeric enzyme from Escherichia coli. The dimeric assembly,
observed also in a previously studied monoclinic crystal form of P. leiognathi
Cu,Zn superoxide dismutase, is based on a ring-shaped subunit contact region,
defining a solvated interface cavity. Three clusters of neighbouring residues
play a direct role in the stabilization of the quaternary assembly. The present
analysis, extended to the amino acid sequences of the other 11 known prokaryotic
Cu,Zn superoxide dismutases, shows that at least in five other prokaryotic
enzymes the interface residue clusters are under strong evolutionary constraint,
suggesting the attainment of a quaternary structure coincident with that of P.
leiognathi Cu,Zn superoxide dismutase. Calculation of electrostatic fields for
both the enzymes from E. coli and P. leiognathi shows that the monomeric/dimeric
association behaviour displayed by prokaryotic Cu, Zn superoxide dismutases is
related to the distribution of surface charged residues. Moreover, Brownian
dynamics simulations reproduce closely the observed enzyme:substrate association
rates, highlighting the role of the active site neighbouring residues in
determining the dismutase catalytic properties.
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Selected figure(s)
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Figure 1.
Figure 1. (a) Stereo view of the C^a traces of the
optimally superimposed three-dimensional structures of PSOD
subunit, ESOD and XSOD (subunit A) represented in blue, orange
and green, respectively. The active site Cu,Zn ions, almost
exactly superimposed, are shown as blue and magenta spheres,
respectively. The molecular regions showing the main structural
differences among the three structures have been labelled. (b)
C^a trace of the dimeric assembly of the prokaryotic PSOD and
(c) of the eukaryotic XSOD. In both cases, the 2-fold axis
relating the two subunits is perpendicular to the plane of the
Figure. The Figure was prepared with the program MOLSCRIPT
[Kraulis 1991].
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Figure 4.
Figure 4. Evolutionary trees for the prokaryotic Cu,Zn SOD
enzymes, deduced (a) from whole amino acid sequence multiple
alignment, and (b) from multiple alignment of only the amino
acids that in PSOD are involved in dimer formation.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
285,
283-296)
copyright 1999.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.I.Lee,
J.W.Lee,
T.C.Yang,
S.O.Kang,
and
B.M.Hoffman
(2010).
ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase.
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J Biol Inorg Chem,
15,
175-182.
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K.C.Ryan,
O.E.Johnson,
D.E.Cabelli,
T.C.Brunold,
and
M.J.Maroney
(2010).
Nickel superoxide dismutase: structural and functional roles of Cys2 and Cys6.
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J Biol Inorg Chem,
15,
795-807.
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M.Calvaresi,
M.Garavelli,
and
A.Bottoni
(2008).
Computational evidence for the catalytic mechanism of glutaminyl cyclase. A DFT investigation.
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Proteins,
73,
527-538.
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R.Krishnakumar,
B.Kim,
E.A.Mollo,
J.A.Imlay,
and
J.M.Slauch
(2007).
Structural properties of periplasmic SodCI that correlate with virulence in Salmonella enterica serovar Typhimurium.
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J Bacteriol,
189,
4343-4352.
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L.Maragliano,
M.Falconi,
A.Sergi,
P.Cioni,
S.Castelli,
A.Lania,
M.E.Stroppolo,
G.Strambini,
M.Ferrario,
and
A.Desideri
(2005).
Experimental and simulative dissociation of dimeric Cu,Zn superoxide dismutase doubly mutated at the intersubunit surface.
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Biophys J,
88,
2875-2882.
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D.H.Kho,
S.B.Yoo,
J.S.Kim,
E.J.Kim,
and
J.K.Lee
(2004).
Characterization of Cu- and Zn-containing superoxide dismutase of Rhodobacter sphaeroides.
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FEMS Microbiol Lett,
234,
261-267.
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L.Spagnolo,
I.Törö,
M.D'Orazio,
P.O'Neill,
J.Z.Pedersen,
O.Carugo,
G.Rotilio,
A.Battistoni,
and
K.Djinovic-Carugo
(2004).
Unique features of the sodC-encoded superoxide dismutase from Mycobacterium tuberculosis, a fully functional copper-containing enzyme lacking zinc in the active site.
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J Biol Chem,
279,
33447-33455.
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PDB code:
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P.A.Doucette,
L.J.Whitson,
X.Cao,
V.Schirf,
B.Demeler,
J.S.Valentine,
J.C.Hansen,
and
P.J.Hart
(2004).
Dissociation of human copper-zinc superoxide dismutase dimers using chaotrope and reductant. Insights into the molecular basis for dimer stability.
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J Biol Chem,
279,
54558-54566.
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R.Gabbianelli,
M.D'Orazio,
F.Pacello,
P.O'Neill,
L.Nicolini,
G.Rotilio,
and
A.Battistoni
(2004).
Distinctive functional features in prokaryotic and eukaryotic Cu,Zn superoxide dismutases.
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Biol Chem,
385,
749-754.
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J.Koca,
C.G.Zhan,
R.C.Rittenhouse,
and
R.L.Ornstein
(2003).
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
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J Comput Chem,
24,
368-378.
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M.Falconi,
M.Brunelli,
A.Pesce,
M.Ferrario,
M.Bolognesi,
and
A.Desideri
(2003).
Static and dynamic water molecules in Cu,Zn superoxide dismutase.
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Proteins,
51,
607-615.
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L.Banci,
I.Bertini,
F.Cramaro,
R.Del Conte,
and
M.S.Viezzoli
(2002).
The solution structure of reduced dimeric copper zinc superoxide dismutase. The structural effects of dimerization.
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Eur J Biochem,
269,
1905-1915.
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PDB code:
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M.Falconi,
L.Parrilli,
A.Battistoni,
and
A.Desideri
(2002).
Flexibility in monomeric Cu,Zn superoxide dismutase detected by limited proteolysis and molecular dynamics simulation.
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Proteins,
47,
513-520.
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M.Falconi,
M.E.Stroppolo,
P.Cioni,
G.Strambini,
A.Sergi,
M.Ferrario,
and
A.Desideri
(2001).
Dynamics-function correlation in Cu, Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study.
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Biophys J,
80,
2556-2567.
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W.S.Valdar,
and
J.M.Thornton
(2001).
Protein-protein interfaces: analysis of amino acid conservation in homodimers.
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Proteins,
42,
108-124.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
