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PDBsum entry 1x9o
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References listed in PDB file
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Key reference
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Title
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A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase.
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Authors
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M.Seto,
M.Whitlow,
M.A.Mccarrick,
S.Srinivasan,
Y.Zhu,
R.Pagila,
R.Mintzer,
D.Light,
A.Johns,
J.A.Meurer-Ogden.
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Ref.
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Protein Sci, 2004,
13,
3172-3186.
[DOI no: ]
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PubMed id
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Abstract
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Sequence profile and fold recognition methods identified mammalian purple acid
phosphatase (PAP), a member of a dimetal-containing phosphoesterase (DMP)
family, as a remote homolog of human acid sphingomyelinase (ASM). A model of the
phosphoesterase domain of ASM was built based on its predicted secondary
structure and the metal-coordinating residues of PAP. Due to the low sequence
identity between ASM and PAP (approximately 15%), the highest degree of
confidence in the model resides in the metal-binding motifs. The ASM model
predicts residues Asp 206, Asp 278, Asn 318, His 425, and His 457 to be dimetal
coordinating. A putative orientation for the phosphorylcholine head group of the
ASM substrate, sphingomyelin (SM), was made based on the predicted catalysis of
the phosphorus-oxygen bond in the active site of ASM and on a structural
comparison of the PAP-phosphate complex to the C-reactive
protein-phosphorylcholine complex. These complexes revealed similar spatial
interactions between the metal-coordinating residues, the metals, and the
phosphate groups, suggesting a putative orientation for the head group in ASM
consistent with the mechanism considerations. A conserved sequence motif in ASM,
NX3CX3N, was identified (Asn 381 to Asn 389) and is predicted to interact with
the choline amine moiety in SM. The resulting ASM model suggests that the enzyme
uses an SN2-type catalytic mechanism to hydrolyze SM, similar to other DMPs. His
319 in ASM is predicted to protonate the ceramide-leaving group in the catalysis
of SM. The putative functional roles of several ASM Niemann-Pick missense
mutations, located in the predicted phosphoesterase domain, are discussed in
context to the model.
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Figure 3.
Figure 3. Secondary structure rendering of the model of the
human ASM phosphodiesterase domain. Secondary structures are
indicated with red barrels (  -helices) and
green arrows (  -sheets). The
amino and carboxyl termini of the domain are labeled with "N"
and "C," respectively. The dimetal center, indicated with a red
arrow, is located within the pseudo twofold symmetry axis of
this domain. The highest confidence region, consisting of the
side chains of five predicted conserved metal-coordinating
residues (D206, D278, N318, H425, and H457) are shown in red.
The metal ions are indicated with pink spheres. The 30-residue
insertion is indicated with a black arrow. (A) The side chains
of the conserved residues with respect to the dimetal center are
shown in purple: N381 and N389 from the NX[3]CX[3]N motif; Asp
210-Tyr 213 and His 282 from the cluster of hydrophilic/aromatic
residues; and C250 and D251 from the CD dipeptide. (B) The side
chains of the Niemann-Pick mutation residues are indicated in
blue in context to the dimetal center: M382, N383, and W391 in
or near the NX[3]CX[3]N motif; H319 in MM3; and L302, P371, and
H421, predicted to lie outside of the dimetal center.
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Figure 5.
Figure 5. Proposed catalytic mechanism for the hydrolysis
of phosphodi-esters by ASM. The active site region of human ASM
is displayed with the metal-coordinating residues. Zinc atoms
are indicated in red. Phosphate is indicated in green. The
bridging hydroxide ion is indicated in blue.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2004,
13,
3172-3186)
copyright 2004.
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