I. Introduction
II. Structure of a Catalase Monomer
III. Quaternary structure: Assembly of the Catalase Tetramer
IV. The Heme Group and its Environment
V. Proposed Mechanism of Catalase
VI. Comparison of Beef Liver and Penicillium Vitale Catalase Structure
VII. Select Catalase WWW Sites
VII. ReferencesNote: This exhibit is best viewed if the cue buttons ( ) are pressed in sequence and if the viewer does not independently manipulate the molecule on the left.
Catalase (EC 1.11.1.6), present in the peroxisomes
of nearly all aerobic cells, serves to protect the cell from
the toxic effects of hydrogen peroxide by catalyzing its decomposition into molecular
oxygen and water without the production of free
radicals. The mechanism of catalysis is not fully elucidated, but the overall
reaction is as follows:
Catalase was one of the first enzymes to be purified to homogeneity, and has been the subject of intense study. The enzyme is among the most efficient known, with rates approaching 200,000 catalytic events/second/subunit (near the diffusion-controlled limit). Catalase structure from many different species has been studied by X-ray diffraction. Although it is clear that all catalases share a general structure, some differ in the number and identity of domains. In this display, beef liver catalase will be used as a model for catalase structure. It will then be compared to catalase structure from a fungus, Penicillium vitale.
Primary structure. Secondary structure. Tertiary structure. The second and largest domain contains the heme
moiety . It is composed of residues 76 to 320 and may be classified as an
a+b type domain. It includes
a b-barrel,
several helical segments of three to four turns
each, and various loops . The b-barrel
consists of two four stranded anti-parallel
b-sheets that twist to form a closed cylindrical surface.
The third domain consists of residues 321-436 and is referred to as the wrapping domain.
It lacks discernable secondary structure except for two
helices , the largest of which (the essential helix) contains the heme
phenolic ligand, Tyr357 .
The carboxy-terminal portion of the molecule contains residues 437 to 506 and is folded
into a four-helical domain similar to the globin
folds. Along with three a-helices
from the heme-containing domain, these helices form one surface of the enzyme
.
The beef liver catalase monomer (shown at left) consists of a 506 amino acid polypeptide
chain plus one heme group and one NADH molecule.
Only about 60% of catalase structure is composed of regular secondary structural
motifs . a-helices
account for 26% of its structure and b-structure
for 12%. Irregular structure includes a predominance
of extended single stands and loops that play a major role in the assembly of
the tetramer.
Each monomer has four domains . The first domain is made up of the amino-terminal 75 residues. These form an arm with
two a-helices
and a large loop extending from the globular subunit
.
Funtional catalase is a tetramer
of four identical holo subunits. A model of a beef liver catalase tetramer
is shown at left. Each monomer harbors a single heme
and NADP. Whereas the
NADPs lie on the surface,
the heme moieties are embedded in the middle of each monomer, ~20 Å below
the molecular surface, and ~23 Å from the center of the tetramer .
The assembly of the multimeric complex is presumably more complicated than
a simple combination of monomers, with changes in the folding pattern of each
monomer occurring so as to optimize packing interactions .
Most intersubunit contacts are confined to the amino-terminal
arms and the wrapping domains . The most flexible parts of the protein are thus responsible for most
of the quaternary structural interactions. The amino-terminal
domain becomes almost completely buried between neighboring subunits in the
tetramer. b-strands
from two pairs of adjacent wrapping domains form inter-subunit anti-parallel
b-sheets
. There are numerous salt bridges at the interfaces between monomers,
mostly involving arginine, asparagine,
and glutamic acid partners . The tetrameric model shown shows a loss of 10633.2 Å2
of solvent accessible surface area upon complex formation!
The Channel to the
Heme Group. The Heme Cavity. The Proximal and Distal Sides of the Heme. The phenolic sidechain of Tyr357 acts
as a the 5th heme iron (Fe) ligand, the other 4
being nitrogens of the heme protoporphyrin ring
(see Introduction). Tyr357
is tightly juxtaposed to the Fe; the Fe-phenolic
oxygen distance is 1.9 Å . As a probable consequence, the phenolic oxygen
is deprotonated due to the electron withdrawing power of Fe.
Arg353 may also promote ionization of Tyr357
by lowering the pKa of the tyrosine phenol (the two sidechains are
only 3.5 Å apart) .
Tyr357 and Arg353
likely interact with other residues, as well. Pro335,
a nonpolar residue, is positioned to impede the movement of Tyr357,
and interaction between Arg353 and His217
may play a role in the catalytic mechanism .
In contrast to the heme's proximal side, its distal side (facing the channel)
is much less confined. It contains many residues,
some of which are contributed by the b-barrel
.
{Note: a group of residues across the b-barrel
function to bind the NADP moiety and include Ser200,
Arg202, Asp212, Lys236, His304,
Val301, Trp302, Tyr214, His234
}.
Phe160 is stacked parallel to one of the heme pyrrole rings
and Val73 makes hydrophobic contact with a different pyrrole ring. His74
is also parallel to the heme, with bond angles
normally allowed for only glycine residues. This conformation is stabilized
by interaction with Arg111 and Thr114
and probably relates directly to enzymatic activity.
As noted above, the heme groups are deeply embedded in each subunit of a modeled
tetramer. However, as can be seen in a monomer
of beef liver catalase, each heme is exposed
through a funnel-shaped channel 30 Å long and
15 Å wide . The channel is lined with hydrophilic residues
at the entrance and with hydrophobic residues as
the channel descends, constricting, toward the heme .
The heme group is located between the internal
wall of the b-barrel
and several helices . The heme pocket is hydrophobic with the exception of a few residues
thought to be involved in binding the prosthetic group or in the catalysis of
of peroxide dismutation (see below).
The proximal (facing the core of the tetramer) and distal (facing the surface)
sides of the heme are quite different environments. The proximal side is crowded
with residues Val145, His 217, Pro
335, Arg353, Ala356,
and Tyr357 . The essential helix of the wrapping
domain (discussed above) provides three of these key residues, Arg353,
Ala356, and Tyr357
.
The chemistry of catalase catalysis has not been precisely solved yet, but the
following, which is similar to the mechanism of cytochrome c peroxidase, has been
proposed. The catalytic process is thought to occur in two stages:
Peroxide, upon entering the heme cavity, is severely sterically hindered and must interact with His74 and Asn147 . It is in this position that the first stage of catalysis takes place. Transfer of a proton from one oxygen of the peroxide to the other, via His74, elongates and polarizes the O-O bond, which eventually breaks heterolytically as a peroxide oxygen is coordinated to the iron center. This coordination displaces water and forms Fe(IV)=O plus a heme radical. The radical quickly degrades in another one electron transfer to rid of the radical electron, leaving the heme ring unaltered. During the second stage, in a similar two electron transfer reaction, Fe(IV)=O reacts with a second hydrogen peroxide to produce the original Fe(III)-E, another water, and a mole of molecular oxygen.
The heme reactivity is enhanced by the phenolate ligand of Tyr357 in the 5th iron ligand position , which may aid in the oxidation of Fe(III) to Fe(IV) and the removal of an electron from the heme ring. The efficiency of catalase may, in part, be due to the interaction of His74 and Asn147 with reaction intermediates. This mechanism is supported by experimental evidence indicating modification of His74 with 3-amino-1,2,4-triazole inhibits the enzyme by hindering substrate binding.
670 residues of Penicillium vitale catalase (PVC) have been built into
a 2 Å resolution electron density map and the backbone of this structure
is compared to that of beef liver catalase (BLC) at
left. The two proteins have many structural similarities, unsurprising given
that they share the same catalytic function. Both catalases, as well as other
catalases, bind heme groups in analogous binding pockets at similar positions.
Both have a tyrosine as a proximal iron ligand, and a distal region containing
a histidine and an asparagine necessary for activity (see above). However, there
are differences in the two structures. PVC has an additional
flavodoxin-like domain
at its carboxy terminus . BLC contains a bound NADP molecule plus an extra 13 residues at the amino-terminus
that are absent in PVC. The NADP molecule in BLC is bound in the region
occupied by the extra flavodoxin-like domain in PVC. The presence of the flavodoxin-like
domain in PVC may indicate the binding of a nucleotide.
The three dimensional structure of proteins is often more conserved than their
amino acid sequences. Comparison of three dimensional structures can reveal
common origins and functions of evolutionarily distant proteins and can provide
information on functionally important, conserved structural features. The above
comparison shows that neither the flavodoxin-like domain of PVC nor the NADP
of BLC are absolutely required for catalase function, but that the presence
of catalase-bound nucleotides is important, presumably to protect the enzyme
from oxidative damage. The structural similarities point to strongly-conserved
mechanisms for peroxide detoxification, since mammalian and fungal catalases
diverged from a common ancestor at least as early as the first eukaryotes.
There is much information about catalase on the world wide web. Here are a few
good starting points:
Mary
Maj's research at Brock University.
Natalia
Snarskaya's site at Moscow State University.
American Cancer Society Publication about catalase
inhibition.
New binding site in catalase?
Test for presence of catalase in oxidant
resistant bacteria.
SCOP: Catalase C-teminal Domain from Penicillium
vitale.
Eventoff, William. (1976) Crystalline Bovine Liver Catalase. J. Mol. Biol. 103, 799-801.
Fita, et al. (1985) The active center of catalase. J. Mol. Biol. 185, 21-37.
Fita, et al. (1986) The refined structure of beef liver catalase. Acta Cryst. B42, 497-515.
Jouve, et al. (1991) Crystallization and crystal packing of Proteus mirabilis PR catalase. J. Mol. Biol. 221, 1075-77.
Mathur, et al. (1981) Structure of beef liver catalase. J. Mol. Biol. 152, 465-99.
Melik-Adamyan, et al. (1986) Comparison of beef liver and Penicillium vitale catalases. J. Mol. Biol. 188, 63-72.
Reid, et al. (1981) Structure and heme environment of beef liver catalase at 2.5 A resolution. Proc. Natl. Acad. Sci. USA 78, 4767-71.
Vainshtein, et al. (1981) Three-dimensional structure of the enzyme catalase. Nature 293, 411-12.
Vainshtein, et al. (1986)
Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution.
J. Mol. Biol. 188, 49-61.
1,
Kenyon College, Gambier, Ohio. A first draft of this exhibit was created for
D. Marcey's Molecular Biology class, Biology 63.
2, Kenyon College, Gambier, Ohio. Present address: California Lutheran University.
Address correspondence to this author (see below).
3, Kenyon College, Gambier, Ohio. This author transferred RasMol script files
into the body of the exhibit text.