PDBsum entry 4bwc

Hydrolase

PDB id: 4bwc

Contents

Protein chains

170 a.a.

321 a.a.

Ligands

NAG-NAG ×3

P4G

NAG ×2

P6G

Metals

_CL

Waters ×184

PDB id:

4bwc

Name:

Hydrolase

Title:

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

Structure:

Phospholipase b-like 1. Chain: a. Fragment: n-terminal segment, residues 36-205. Synonym: lama-like protein 1, lamina ancestor homolog 1, phospholipase b domain-containing protein 1, phospholipase b-like protein 1. Phospholipase b-like 1. Chain: b. Fragment: c-terminal segment, residues 225-545.

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Organ: kidney. Organ: kidney

Resolution:

1.89Å R-factor: 0.190 R-free: 0.231

Authors:

H.Repo,E.Kuokkanen,E.Oksanen,A.Goldman,P.Heikinheimo

Key ref:

H.Repo et al. (2014). Is the bovine lysosomal phospholipase B-like protein an amidase? Proteins, 82, 300-311. PubMed id: 23934913 DOI: 10.1002/prot.24388

Date:

01-Jul-13 Release date: 18-Sep-13

Protein chain

Q9GL30  (PLBL1_BOVIN) -  Phospholipase B-like 1 from Bos taurus

Seq: 545 a.a.

Struc: 170 a.a.

Protein chain

Q9GL30  (PLBL1_BOVIN) -  Phospholipase B-like 1 from Bos taurus

Seq: 545 a.a.

Struc: 321 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.1.1.- - ?????

DOI no: 10.1002/prot.24388

Proteins 82:300-311 (2014)

PubMed id: 23934913

Is the bovine lysosomal phospholipase B-like protein an amidase?

H.Repo, E.Kuokkanen, E.Oksanen, A.Goldman, P.Heikinheimo.

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. Proteins 2014; 82:300-311. © 2013 Wiley Periodicals, Inc.