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monoamine oxidase B,
a drug target for the BENZYLAMINE PHENETHYLAMINE
treatment of neurological N
disorders
© 2002 Nature Publishing Group http://structbio.nature.com
N CH3 HO
Fig. 2 Stereo view of the experimental electron density map. The map
was obtained by 12-fold averaging over two crystal forms at 3.0 Å reso-
lution. The contour level is 1.0 σ. Carbons are in black, nitrogens in blue,
oxygens in red and sulfurs in yellow. The figure shows the active site with
the flavin ring covalently bound to Sγ of Cys 397 and the pargyline
inhibitor covalently attached to the N5 atom of the FAD cofactor. The
flavin ring is in a bent, twisted conformation, with an angle of 26°
between the planes of the benzenoid and pyrimidine rings.
© 2002 Nature Publishing Group http://structbio.nature.com
Overall structure of human MAO B efficient detergent extraction13. The protein region responsible
The 520 amino acids of MAO B fold into a compact structure for membrane attachment is formed by the C-terminal amino
(Fig. 3a) that exhibits a topology initially found in p-hydroxy-acids 461–520 (ref. 1). Analysis of the MAO B amino acid
benzoate hydroxylase and then observed in several flavopro- sequence with the program TopPred14 predicts that residues
teins9. A search of the Protein Data Bank10 reveals that the closest
489–515 form a transmembrane helix 27 amino acids long,
structural matches of MAO B are L-amino acid oxidase11 and which is well within the range of values observed for transmem-
polyamine oxidase12, with root mean square (r.m.s.) deviations brane helices in membrane proteins of known three-dimension-
of 2.7 Å (420 Cα atoms with 22% sequence identity) and 3.5 Å al structure15. MAO B is expected to contain additional
(404 Cα atoms with 18% sequence identity), respectively. membrane interaction sites, because C-terminal truncation
mutagenesis experiments (ref.16; P.N.-V. and D.E.E., unpub-
The crystal structure shows that the enzyme is dimeric (Fig. 3a),
lished data) show that various deletions of the C-terminal
which is unlikely to be a crystal packing artifact because the dimer
is present in the two crystal forms (orthorhombic and triclinic)residues do not completely abolish the ability of the enzyme to
employed in the structure determination (Table 1; Methods). bind to the membrane.
Indeed, the monomer–monomer interactions are extensive; The crystal structure reveals that the C-terminal residues form
2,095 Å2 of the surface area (15% of monomer accessible surface)an extended polypeptide chain (amino acids 461–488) that tra-
is buried upon dimer formation. Therefore, the dimer form is sug-
verses the monomer surface (Fig. 3a). This extended chain is fol-
gested to be the quaternary assembly present in vivo. lowed by an α-helix that initiates at Val 489, forming the
predicted transmembrane helical segment (Fig. 3a,b). The helix
Structure of the membrane binding region of each monomer protrudes from the basal face of the dimer
MAO B is tightly bound to the outer mitochondrial membrane, (when oriented as in Fig. 3a), with each helical axis approxi-
as evidenced by the need for digestion of phospholipids for its mately parallel to the molecular two-fold axis. This observation
a b c
Fig. 3 Structure of human MAO B. a, Ribbon diagram of the MAO B dimer with the two-fold axis vertical in the plane of the paper. Monomer A is on
the right and monomer B is on the left. The letters ‘N’ and ‘C’ indicate the observed N-terminal (Lys 4 in both monomers) and C-terminal (Thr 500 in
monomer A and Ile 496 in monomer B) amino acids, respectively. Residues 4–460 are in red, and the C-terminal tail (residues 461–500) is in green. The
dimer is anchored to the outer mitochondrial membrane through the C-terminal tails and the neighboring residues of each monomer. The molecu-
lar two-fold axis is perpendicular to the membrane plane, allowing equivalent interactions between each monomer and the membrane. The FAD is
shown in ball-and-stick representation and colored in yellow. The membrane region boundary is indicated by a thick dashed line for illustration pur-
poses and is not intended to define the exact depth of protein insertion into the membrane. b, Close-up view of the membrane binding region in
monomer A. The orientation and the color scheme for the backbone trace are as in (a). To allow visualization of all side chains, the ribbon for the
C-terminal residues (green) has been made semitransparent. Carbons are in black, nitrogens in blue and oxygens in red. The amino-acid sequence of
the C-terminal residues (480–520) is indicated. Residues 489–515 (predicted to form the transmembrane helix) are underlined. Residues 501–520
were not included in the final model because they are not well defined in the electron density. c, Cavities constituting the substrate path from the
protein surface to the flavin in the MAO B monomer. Adjacent to the active site cavity (cyan) is the ‘entrance’ cavity (blue), which is underneath loop
99–112. The FAD is in yellow and the covalent pargyline inhibitor is in black. The color scheme of (a) is used. With respect to (a), the model has been
rotated by 90° around the vertical axis in the plane of the paper.
a b
© 2002 Nature Publishing Group http://structbio.nature.com
Fig. 4 The substrate binding site of human MAO B. a, Stereo view of the pargyline inhibitor and the residues lining the binding site at the re side of
the flavin. Carbons are in black, nitrogens in blue, oxygens in red and sulfurs in yellow. The inhibitor is outlined by shaded bonds. With respect to
Fig. 3c, the model has been rotated by 90° around an axis approximately orthogonal to the plane of the paper. b, Schematic representation of the
pargyline binding site. MAO B residues that are conserved in human MAO A are indicated by an asterisk. For nonconserved amino acids, the replace-
ment side chains of MAO A are in parentheses. Aromatic side chains are enclosed in ellipsoidal frames. Other residues are in rectangular boxes. The
atoms of the flavin ring are numbered. c, A model for the binding of the substrate, benzylamine, to human MAO B. For illustrative purposes, the
atoms and bonds of the modeled substrate are shown in an increased size. The surface of the solvent inaccessible substrate-binding cavity is semi-
transparent. For clarity, only some of the residues lining the cavity are depicted. Carbons are in cyan, nitrogens in blue and oxygens in red. The ori-
entation is as in (a). The reactive N5 site on the twisted flavin ring is labeled.
suggests that the dimer binds to the membrane with its two-fold dicted by substrate specificity and quantitative structure-activity
axis perpendicular to the membrane plane, and the C-terminal relationship (QSAR) studies17.
helices inserted in the lipid bilayer. In a second helix turn, Adjacent to the substrate cavity is a separate, smaller
Arg 494 is oriented in the proper direction for electrostatic inter- hydrophobic cavity (volume of 290 Å3) lined by residues
action with the anionic phospholipid headgroups (Fig. 3b), Phe 103, Pro 104, Trp 119, Leu 164, Leu 167, Phe 168, Leu 171,
which is often observed in transmembrane helices15. Although Ile 199, Ile 316 and Tyr 326. This second cavity is situated
the C-terminal helix is predicted to extend to residue 515, the between the active site and the protein surface, and is shielded
electron density in this region is interrupted at Thr 500 in from solvent by loop 99–112 (Fig. 3c). Residues Tyr 326, Ile 199,
monomer A (Fig. 3b) and at Ile 496 in monomer B. Static and/or Leu 171 and Phe 168 are the side chains that separate the two
dynamic disorder in this portion of the helix may result from the cavities. These observations suggest a mechanism for admission
absence of the membrane bilayer. of the substrate into the active site that initially involves the
In addition to the C-terminal helical segment, the structure movement of loop 99–112 to open access to the smaller cavity
shows that other protein regions may be involved in membrane (termed the ‘entrance cavity’). After substrate reaches the
binding (Fig. 3b). In residues 481–488 of the elongated polypep- ‘entrance cavity’, a transient movement of the four residues sepa-
tide stretch preceding the C-terminal helix, several hydrophobic rating the entrance from the substrate cavities must occur to
side chains (Phe 481, Leu 482, Leu 486 and Pro 487) point allow its diffusion into the active site. The total distance of sub-
towards the membrane. At the end of loop 99–112 (Fig. 3b,c), strate migration from the surface of the entrance cavity to the
Pro 109 and Ile 110 are surface-exposed in a position that could flavin ring is ∼20 Å. Loop 99–112 may function as a ‘gating
allow interaction with the membrane. The current structural switch’ to the entrance cavity. The loop is situated proximal to
data do not define the exact depth of protein insertion into the the membrane binding region (Fig. 3c), suggesting that sub-
bilayer. However, the presence of these exposed hydrophobic strate must access the catalytic site from the protein surface ori-
side chains suggests that membrane attachment does not solely ented towards the membrane.
involve the C-terminal helix but also additional hydrophobic
patches of the protein surface. Structural basis of catalysis
To analyze the mechanistic implications of the MAO B three-
The active site dimensional structure, we have attempted to model the binding
The electron density map (Fig. 2) shows that pargyline covalent- of substrate in the active site. Benzylamine (Fig. 1b) was chosen
ly binds to the N5 atom on the re side of the flavin in a solvent because there are considerable data on the interaction of this
inaccessible environment. The substrate binding site is formed substrate and its analogs with the enzyme17. Comparison of
by a flat cavity with a volume of 420 Å3 (Fig. 3c). This cavity is flavoenzyme three-dimensional structures9 has revealed that the
lined by a number of aromatic and aliphatic amino acids substrate carbon atom undergoing flavin-dependent oxidation
(Fig. 4a,b), providing the highly hydrophobic environment pre- binds in a highly conserved position in front of the flavin
N5–C4a locus9. On this basis, the benzylamine methylene car- Substrate specificities of MAOs
bon was positioned 3.6 Å from flavin N5. The orientation of the Human MAO A and MAO B share a high sequence identity
aromatic ring was restricted by the flat shape of the cavity (∼70%) but differ in their substrate specificities. MAO B mainly
(Fig. 4c). As a result, the amine binds between the phenolic side acts on small exogenous amines, whereas MAO A carries out the
chains of Tyr 398 and Tyr 435 (edge to edge distance of 7.8 Å). degradation of bulkier endogenous amine neurotransmitters,
These residues, together with the flavin, form an aromatic caged such as serotonin (Fig. 1a). The differences between human
environment (Fig. 4a,c) that is responsible for recognition of the MAO B and MAO A in residues lining the substrate cavity
amino group. No interaction of the substrate nitrogen atom with (Fig. 4b) include Leu 171 (MAO B)/Ile 180 (MAO A),
any anionic residues is detected, which agrees with the known Cys 172/Asn 181, Ile 199/Phe 208 and Tyr 326/Ile 335. These
preference of MAO to bind the deprotonated substrate18. An aro- amino acids are located in the rear of the substrate cavity
matic cage similar to that of MAO B is also observed in two other (Fig. 4a,b) in van der Waals contact with the benzene ring of
pargyline. Three of the four residues (Leu 171, Ile 199 and metry (NCS)-related subunits were subjected to tight NCS restraints
Tyr 326) separate the substrate cavity from the entrance cavity. throughout the refinement. The final model (residues 4–500 for
Thus, side chain changes in these positions affect not only steric monomer A and 4–496 for monomer B) has an R-factor of 23.0%
and an Rfree of 27.1%, with good stereochemical parameters
accomodation of the substrate but may also lead to alterations in (Table 1). Four residues in each subunit are in disallowed regions of
the separation of the substrate cavity from the entrance cavity. the Ramachandran plot, one of which is Tyr 398 of the active center
By altering the side chains of these residues, the two cavities may (Table 1). Refinement of the model in the triclinic crystal form is cur-
fuse to form a single larger cavity that would accommodate larg- rently in progress and will be described elsewhere together with a
er substrates and inhibitors, as observed for MAO A. Mutations more detailed analysis of MAO B structure. Volume calculations
were performed with VOIDOO31 using a probe radius of 1.4 Å.
© 2002 Nature Publishing Group http://structbio.nature.com