 |
PDBsum entry 1xdc
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
1xdc
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Oxidoreductase
|
|
|
Title:
|
|
Hydrogen bonding in human manganese superoxide dismutase containing 3- fluorotyrosine
|
|
Structure:
|
|
Superoxide dismutase [mn], mitochondrial. Chain: a, b. Engineered: yes
|
|
Source:
|
|
Homo sapiens. Human. Organism_taxid: 9606. Gene: sod2. Expressed in: escherichia coli. Expression_system_taxid: 562.
|
|
Biol. unit:
|
|
Tetramer (from PDB file)
|
|
Resolution:
|
|
|
1.85Å
|
R-factor:
|
0.212
|
R-free:
|
0.252
|
|
|
Authors:
|
|
I.Ayala,J.J.Perry,J.Szczepanski,D.E.Cabelli,J.A.Tainer,M.T.Vala, H.S.Nick,D.N.Silverman
|
|
Key ref:
|
|
I.Ayala
et al.
(2005).
Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine.
Biophys J,
89,
4171-4179.
PubMed id:
|
|
|
Date:
|
|
|
05-Sep-04
|
Release date:
|
22-Mar-05
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P04179
(SODM_HUMAN) -
Superoxide dismutase [Mn], mitochondrial from Homo sapiens
|
|
|
|
Seq:
Struc:
|
|
|
|
222 a.a.
198 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
*
PDB and UniProt seqs differ
at 9 residue positions (black
crosses)
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.1.15.1.1
- superoxide dismutase.
|
|
|
|
|
|
|
Reaction:
|
|
2 superoxide + 2 H+ = H2O2 + O2
|
|
|
|
|
|
2
×
superoxide
|
+
|
2
×
H(+)
|
=
|
H2O2
|
+
|
O2
|
|
|
|
|
|
|
|
|
|
Cofactor:
|
|
Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
|
Biophys J
89:4171-4179
(2005)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine.
|
|
I.Ayala,
J.J.Perry,
J.Szczepanski,
J.A.Tainer,
M.T.Vala,
H.S.Nick,
D.N.Silverman.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Incorporation of 3-fluorotyrosine and site-specific mutagenesis has been
utilized with Fourier transform infrared (FTIR) spectroscopy and x-ray
crystallography to elucidate active-site structure and the role of an
active-site residue Tyr34 in human manganese superoxide dismutase (MnSOD).
Calculated harmonic frequencies at the B3LYP/6-31G** level of theory for
L-tyrosine and its 3-fluorine substituted analog are compared to experimental
frequencies for vibrational mode assignments. Each of the nine tyrosine residues
in each of the four subunits of the homotetramer of human MnSOD was replaced
with 3-fluorotyrosine. The crystal structures of the unfluorinated and
fluorinated wild-type MnSOD are nearly superimposable with the root mean-square
deviation for 198 alpha-carbon atoms at 0.3 A. The FTIR data show distinct
vibrational modes arising from 3-fluorotyrosine in MnSOD. Comparison of spectra
for wild-type and Y34F MnSOD showed that the phenolic hydroxyl of Tyr34 is
hydrogen bonded, acting as a proton donor in the active site. Comparison with
crystal structures demonstrates that the hydroxyl of Tyr34 is a hydrogen bond
donor to an adjacent water molecule; this confirms the participation of Tyr34 in
a network of residues and water molecules that extends from the active site to
the adjacent subunit.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
F.Rappaport,
A.Boussac,
D.A.Force,
J.Peloquin,
M.Brynda,
M.Sugiura,
S.Un,
R.D.Britt,
and
B.A.Diner
(2009).
Probing the coupling between proton and electron transfer in photosystem II core complexes containing a 3-fluorotyrosine.
|
| |
J Am Chem Soc,
131,
4425-4433.
|
|
|
|
|
|
|
J.J.Perry,
A.S.Hearn,
D.E.Cabelli,
H.S.Nick,
J.A.Tainer,
and
D.N.Silverman
(2009).
Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.
|
| |
Biochemistry,
48,
3417-3424.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
G.Cornilescu,
E.B.Hadley,
M.G.Woll,
J.L.Markley,
S.H.Gellman,
and
C.C.Cornilescu
(2007).
Solution structure of a small protein containing a fluorinated side chain in the core.
|
| |
Protein Sci,
16,
2089.
|
|
|
|
|
|
|
J.J.Perry,
L.Fan,
and
J.A.Tainer
(2007).
Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.
|
| |
Neuroscience,
145,
1280-1299.
|
|
|
|
|
|
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
codes are
shown on the right.
|
|
Links
