4BWC

X-ray structure of a phospholiapse B like protein 1 from bovine kidneys

Summary for 4BWC

• Entry DOI: 10.2210/pdb4bwc/pdb
• Descriptor: PHOSPHOLIPASE B-LIKE 1, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE, ... (8 entities in total)
• Functional Keywords: hydrolase, glycosylation, lysosomal storage disorders
• Biological source: BOS TAURUS (BOVINE); More
• Total number of polymer chains: 2
• Total formula weight: 58878.06

Authors

Repo, H.,Kuokkanen, E.,Oksanen, E.,Goldman, A.,Heikinheimo, P. (deposition date: 2013-07-01, release date: 2013-09-18, Last modification date: 2023-12-20)

Primary citation

Repo, H.,Kuokkanen, E.,Oksanen, E.,Goldman, A.,Heikinheimo, P.
Is the Bovine Lysosomal Phospholipase B-Like Protein an Amidase?
Proteins, 82:300-, 2014

PubMed Abstract: 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.

PubMed: 23934913
DOI: 10.1002/PROT.24388

Experimental method

X-RAY DIFFRACTION (1.89 Å)