PDBsum entry 2agc

Lipid binding protein

PDB id: 2agc

Contents

Protein chain

162 a.a.

Ligands

MYR

DAO ×2

Waters ×66

References listed in PDB file

Key reference

Title

Crystal structure analysis of phosphatidylcholine-Gm2-Activator product complexes: evidence for hydrolase activity.

Authors

C.S.Wright, L.Z.Mi, S.Lee, F.Rastinejad.

Ref.

Biochemistry, 2005, 44, 13510-13521. [DOI no: 10.1021/bi050668w]

PubMed id

16216074

Abstract

GM2-activator protein (GM2AP) is a lysosomal lipid transfer protein with important biological roles in ganglioside catabolism, phospholipid metabolism, and T-cell activation. Previous studies of crystal structures of GM2AP complexed with the physiological ligand GM2 and platelet activating factor (PAF) have shown binding at two specific locations within the spacious apolar pocket and an ordering effect of endogenous resident lipids. To investigate the structural basis of phospholipid binding further, GM2AP was cocrystallized with phosphatidylcholine (PC), known to interact with GM2AP. Analysis of three crystal forms revealed binding of single chain lipids and fatty acids only and surprisingly not intact PC. The regions of best defined electron density are consistent with the presence of lyso-PC and oleic acid, which constitute deacylation products of PC. Their acyl tails are in stacking contact with shorter, less well-defined stretches of electron density that may represent resident fatty acids. The GM2AP associated hydrolytic activity that generates lyso-PC was further confirmed by mass spectrometry and enzymatic assays. In addition, we report the structures of (i) mutant Y137S, assessing the role of Tyr137 in lipid transfer via the hydrophobic cleft, and (ii) apo-mouse GM2AP, revealing a hydrophobic pocket with a constricted opening. Our structural results provide new insights into the biological functions of GM2AP. The combined effect of hydrolytic and lipid transfer properties has profound implications in cellular signaling.

Secondary reference #1

Title

Crystal structure of human gm2-Activator protein with a novel beta-Cup topology.

Authors

C.S.Wright, S.C.Li, F.Rastinejad.

Ref.

J Mol Biol, 2000, 304, 411-422. [DOI no: 10.1006/jmbi.2000.4225]

PubMed id

11090283

Figure 4.
Figure 4. The lipophilic cavity. (a) Stereoscopic view displaying all hydrophobic side-chains inside the b-cup. (b) Stereoscopic view of the three independent monomers superimposed using the program LSQKAB (CCP4 suite). The monomers are color-coded red (monomer A), yellow (monomer B) and blue (monomer C). Regions of high flexibility are A90-D100, I119-C125, F152-L163. Side-chains with the largest rmsd among the three monomers (see the text) are displayed with the same color code (Figures generated with RIBBONS).[42]

Figure 5.
Figure 5. GRASP representation of the electrostatic surface potential of the GM2-AP monomer viewing into the hydrophobic cavity.[44] The depth of the central hydrophobic cavity is apparent from the dark grey shading. Regions shown in red and blue represent amino acid residues with a negative and positive electrostatic potential, respectively. The regions of structural changes, as discussed in the text, are labeled.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Structural analysis of lipid complexes of gm2-Activator protein.

Authors

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

Ref.

J Mol Biol, 2003, 331, 951-964. [DOI no: 10.1016/S0022-2836(03)00794-0]

PubMed id

12909021

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 reproduced from the cited reference with permission from Elsevier

Secondary reference #3

Title

Evidence for lipid packaging in the crystal structure of the gm2-Activator complex with platelet activating factor.

Authors

C.S.Wright, L.Z.Mi, F.Rastinejad.

Ref.

J Mol Biol, 2004, 342, 585-592. [DOI no: 10.1016/j.jmb.2004.07.063]

PubMed id

15327957

Figure 1.
Figure 1. Stereo view comparing the structures of crystallographically distinct monomers. Superpositions were carried out with the program LSQKAB.27 Monomers A, B and C of PAF-GM2-AP are shown in cyan, blue and magenta, respectively. The flexible reverse turn P129 to L132 is labeled mobile loop. The protruding loop V59 to W63, thought to interact with lipid bilayers, is labeled apolar loop. Monomer C of the apo structure is shown superimposed in yellow, illustrating the rotated position of the mobile loop with insertion of W131 into the cleft. N and C refer to the amino and carboxy terminal ends of the polypeptide chain. The position of the chloride ion (CL) is indicated. Sequence numbering refers to the mature protein of 162 amino acid residues. The Figure was generated with Dino (http://cobra.mih.unibas.ch/dino).

Figure 5.
Figure 5. Comparison of the bound conformations of PAF and lyso-PAF in monomers A (grey), B (yellow) and C (green). PAF binds within the hydrophobic cleft at position I and lyso-PAF binds inside the pocket at position II. The acetate ion is labeled AC. The Figure was generated with DINO.

The above figures are reproduced from the cited reference with permission from Elsevier