PDBsum entry 1pub

Lipid binding protein

PDB id: 1pub

Contents

Protein chain

162 a.a. *

Ligands

3PH

Waters ×61

* Residue conservation analysis

PDB id:

1pub

Name:

Lipid binding protein

Title:

Gm2-activator protein crystal structure

Structure:

Gm2-activator protein. Chain: a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.51Å R-factor: 0.209 R-free: 0.286

Authors:

C.S.Wright,Q.Zhao,F.Rastinejad

Key ref:

C.S.Wright et al. (2003). Structural analysis of lipid complexes of GM2-activator protein. J Mol Biol, 331, 951-964. PubMed id: 12909021 DOI: 10.1016/S0022-2836(03)00794-0

Date:

24-Jun-03 Release date: 29-Jun-04

Protein chain

P17900  (SAP3_HUMAN) -  Ganglioside GM2 activator from Homo sapiens

Seq: 193 a.a.

Struc: 162 a.a.

DOI no: 10.1016/S0022-2836(03)00794-0

J Mol Biol 331:951-964 (2003)

PubMed id: 12909021

Structural analysis of lipid complexes of GM2-activator protein.

C.S.Wright, Q.Zhao, F.Rastinejad.

ABSTRACT

The GM2-activator protein (GM2-AP) is a small lysosomal lipid transfer protein essential for the hydrolytic conversion of ganglioside GM2 to GM3 by beta-hexosaminidase A. The crystal structure of human apo-GM2-AP is known to consist of a novel beta-cup fold with a spacious hydrophobic interior. Here, we present two new structures of GM2-AP with bound lipids, showing two different lipid-binding modes within the apolar pocket. The 1.9A structure with GM2 bound shows the position of the ceramide tail and significant conformational differences among the three molecular copies in the asymmetric unit. The tetrasaccharide head group is not visible and is presumed to be disordered. However, its general position could be established through modeling. The structure of a low-pH crystal, determined at 2.5A resolution, has a significantly enlarged hydrophobic channel that merges with the apolar pocket. Electron density inside the pocket and channel suggests the presence of a trapped phospholipid molecule. Structure alignments among the four crystallographically unique monomers provide information on the potential role for lipid binding of flexible chain segments at the rim of the cavity opening. Two discrete orientations of the S130-T133 loop define an open and a closed configuration of the hydrophobic channel that merges with the apolar pocket. We propose: (i) that the low-pH structure represents an active membrane-binding conformation; (ii) that the mobile S130-T133 loop serves as a gate for passage of ligand into the apolar pocket; and (iii) that this loop and the adjacent apolar V59-W63 loop form a surface patch with two exposed tryptophan residues that could interface with lipid bilayers.

Selected figure(s)

Figure 2.
Figure 2. A stereoscopic view of the two positions of the mobile W131 loop observed in GM2-AP3. The stick models are color-coded blue for monomer A with the loop in the exposed position, and magenta for monomer C with the loop folded in making contact with hydrophobic residues (shown in yellow). The broken line indicates the invariant hydrogen bond between the carbonyl oxygen atom of T133 and the OH group of Y137, and the arrow points at the C^a-CO bond of T133, serving as a flexible hinge with the C-terminal T134 fixed. The Figure was generated with DINO.

Figure 6.
Figure 6. A representation of the proposed interaction of GM2-AP with a lipid monolayer. The open structure of GM2-AP1 is depicted as ribbon model (generated in DINO) with its apolar and mobile loops colored purple. Basic amino acid side-chains in this region are shown in blue (K57, K65, R138, K154), and the two tryptophan residues (W63, W131) are shown in yellow. In structure A, the apolar loop is shown to interface with a PC monolayer. Structure B represents the observed crystal complex of GM2-AP1.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 951-964) copyright 2003.

Figures were selected by an automated process.