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PDBsum entry 4bwc
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References listed in PDB file
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Key reference
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Title
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Is the bovine lysosomal phospholipase b-Like protein an amidase?
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Authors
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H.Repo,
E.Kuokkanen,
E.Oksanen,
A.Goldman,
P.Heikinheimo.
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Ref.
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Proteins, 2014,
82,
300-311.
[DOI no: ]
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PubMed id
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Abstract
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The main function of lysosomal proteins is to degrade cellular macromolecules.
We purified a novel lysosomal protein to homogeneity from bovine kidneys. By
gene annotation, this protein is defined as a bovine phospholipase B-like
protein 1 (bPLBD1) and, to better understand its biological function, we solved
its structure at 1.9 Å resolution. We showed that bPLBD1 has uniform
noncomplex-type N-glycosylation and that it localized to the lysosome. The first
step in lysosomal protein transport, the initiation of mannose-6-phosphorylation
by a N-acetylglucosamine-1-phosphotransferase, requires recognition of at least
two distinct lysines on the protein surface. We identified candidate lysines by
analyzing the structural and sequentially conserved N-glycosylation sites and
lysines in bPLBD1 and in the homologous mouse PLBD2. Our model suggests that
N408 is the primarily phosphorylated glycan, and K358 a key residue for
N-acetylglucosamine-1-phosphotransferase recognition. Two other lysines, K334
and K342, provide the required second site for
N-acetylglucosamine-1-phosphotransferase recognition. bPLBD1 is an N-terminal
nucleophile (Ntn) hydrolase. By comparison with other Ntn-hydrolases, we
conclude that the acyl moiety of PLBD1 substrate must be small to fit the
putative binding pocket, whereas the space for the rest of the substrate is a
large open cleft. Finally, as all the known substrates of Ntn-hydrolases have
amide bonds, we suggest that bPLBD1 may be an amidase or peptidase instead of
lipase, explaining the difficulty in finding a good substrate for any members of
the PLBD family. Proteins 2014; 82:300-311. © 2013 Wiley Periodicals, Inc.
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