 |
PDBsum entry 1cf9
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
1cf9
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Mutants that alter the covalent structure of catalase hydroperoxidase ii from escherichia coli.
|
|
|
Authors
|
|
M.J.Maté,
M.S.Sevinc,
B.Hu,
J.Bujons,
J.Bravo,
J.Switala,
W.Ens,
P.C.Loewen,
I.Fita.
|
|
|
Ref.
|
|
J Biol Chem, 1999,
274,
27717-27725.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The three-dimensional structures of two HPII variants, V169C and H392Q, have
been determined at resolutions of 1.8 and 2.1 A, respectively. The V169C variant
contains a new type of covalent bond between the sulfur atom of Cys(169) and a
carbon atom on the imidazole ring of the essential His(128). This variant enzyme
has only residual catalytic activity and contains heme b. The chain of water
molecules visible in the main channel may reflect the organization of the
hydrogen peroxide substrates in the active enzyme. Two alternative mechanisms,
involving either compound I or free radical intermediates, are presented to
explain the formation of the Cys-His covalent bond. The H392Q and H392E variants
exhibit 75 and 25% of native catalytic activity, respectively. The Gln(392)
variant contains only heme b, whereas the Glu(392) variant contains a mixture of
heme b and cis and trans isomers of heme d, suggesting of a role for this
residue in heme conversion. Replacement of either Gln(419) and Ser(414), both of
which interact with the heme, affected the cis:trans ratio of spirolactone heme
d. Implications for the heme oxidation mechanism and the His-Tyr bond formation
in HPII are considered.
|
|
|
|
|
|
|
|
Figure 5.
Fig. 5. Reversed-phase HPLC chromatograms for the heme
isolated from HPII catalase (A) and the mutant variants H392Q
(B), H392E (C), Q419H (D), and S414A (E). The peaks of heme d
are indicated by d and the peak of heme b is indicated by b. The
faster eluting peak of heme d is the cis isomer and the slower
eluting peak is the trans isomer.
|
|
Figure 6.
Fig. 6. Possible mechanisms for the formation of the
covalent bond found in the V169C variant of HPII between the
mutated residue Cys169 and the essential histidine His128.
Scheme A shows the proposed nucleophilic mechanism based on the
acid catalyzed nucleophilic addition of the thiol group of
Cys169 onto the imidazole ring of His128. Scheme B shows an
alternate mechanism where protonation of His128, in the initial
step of compound I formation, triggers the nucleophilic attack
of the thiol group of Cys169 on the imidazole ring. Scheme C
depicts the proposed free radical mechanism based on the
oxidation of the thiol group of Cys169 to yield a thiyl radical
which can attack the imidazolic system.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1999,
274,
27717-27725)
copyright 1999.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystal structure of catalase hpii from escherichia coli.
|
|
|
Authors
|
|
J.Bravo,
N.Verdaguer,
J.Tormo,
C.Betzel,
J.Switala,
P.C.Loewen,
I.Fita.
|
|
|
Ref.
|
|
Structure, 1995,
3,
491-502.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 2.
Figure 2. Representative stereoviews of the final averaged
(2F[o]–F[c]) electron-density map. Residues (a) Ile274 and (b)
His739 are outside energetically favorable regions in the
Ramachandran diagram (see Figure 3). The identification of the
bulky residue Trp742 (b) facilitated the tracing of the
C-terminal domain. (c) Exposed segment in the hinge region,
including residues Pro575-Pro576-Pro577. Figure 2.
Representative stereoviews of the final averaged (2F[o]–F[c])
electron-density map. Residues (a) Ile274 and (b) His739 are
outside energetically favorable regions in the Ramachandran
diagram (see [5]Figure 3). The identification of the bulky
residue Trp742 (b) facilitated the tracing of the C-terminal
domain. (c) Exposed segment in the hinge region, including
residues Pro575-Pro576-Pro577.
|
|
Figure 10.
Figure 10. Stereoview of the electron density in the terminal
carboxylate environment (residue Ala753). The molecular dyad
R-axis-related residues are shown with thinner bonds. The
terminal carboxylate charged group appears to be neutralized by
Lys309. Figure 10. Stereoview of the electron density in the
terminal carboxylate environment (residue Ala753). The molecular
dyad R-axis-related residues are shown with thinner bonds. The
terminal carboxylate charged group appears to be neutralized by
Lys309.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from Cell Press
|
|
|
Secondary reference #2
|
|
|
Title
|
|
2.8 a crystal structure of catalase hpii from escherichia coli
|
|
|
Authors
|
|
J.Bravo,
N.Verdaguer,
J.Tormo,
C.Betzel,
J.Switala,
P.C.Loewen,
I.Fita.
|
|
|
Ref.
|
|
joint ccp4 esf-eacbm, 1993,
28,
79.
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
Crystallization and preliminary X-Ray diffraction analysis of catalase hpii from escherichia coli.
|
|
|
Authors
|
|
J.Tormo,
I.Fita,
J.Switala,
P.C.Loewen.
|
|
|
Ref.
|
|
J Mol Biol, 1990,
213,
219-220.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
The refined structure of beef liver catalase at 2.5 a resolution
|
|
|
Authors
|
|
I.Fita,
A.M.Silva,
M.R.N.Murthy,
M.G.Rossmann.
|
|
|
Ref.
|
|
acta crystallogr ,sect b, 1986,
42,
497.
|
|
|
|
|
|
|
|
