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2ag2, resolution 2.00Å ()
Ligands: , , , , , , ,
Gene: GM2A (Homo sapiens)
Related: 1g13, 1pub, 1pu5, 1tjj
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine

Publication Abstract from PubMed

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.

Crystal structure analysis of phosphatidylcholine-GM2-activator product complexes: evidence for hydrolase activity., Wright CS, Mi LZ, Lee S, Rastinejad F, Biochemistry. 2005 Oct 18;44(41):13510-21. PMID:16216074

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.


[SAP3_HUMAN] Defects in GM2A are the cause of GM2-gangliosidosis type AB (GM2GAB) [MIM:272750]; also known as Tay-Sachs disease AB variant. GM2-gangliosidosis is an autosomal recessive lysosomal storage disease marked by the accumulation of GM2 gangliosides in the neuronal cells. GM2GAB is characterized by GM2 gangliosides accumulation in the presence of both hexosaminidase A and B.[1][2][3]


[SAP3_HUMAN] The large binding pocket can accommodate several single chain phospholipids and fatty acids, GM2A also exhibits some calcium-independent phospholipase activity (By similarity). Binds gangliosides and stimulates ganglioside GM2 degradation. It stimulates only the breakdown of ganglioside GM2 and glycolipid GA2 by beta-hexosaminidase A. It extracts single GM2 molecules from membranes and presents them in soluble form to beta-hexosaminidase A for cleavage of N-acetyl-D-galactosamine and conversion to GM3.

About this Structure

2ag2 is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.


  • Wright CS, Mi LZ, Lee S, Rastinejad F. Crystal structure analysis of phosphatidylcholine-GM2-activator product complexes: evidence for hydrolase activity. Biochemistry. 2005 Oct 18;44(41):13510-21. PMID:16216074 doi:http://dx.doi.org/10.1021/bi050668w
  • Wright CS, Li SC, Rastinejad F. Crystal structure of human GM2-activator protein with a novel beta-cup topology. J Mol Biol. 2000 Dec 1;304(3):411-22. PMID:11090283 doi:http://dx.doi.org/10.1006/jmbi.2000.4225
  • Wright CS, Zhao Q, Rastinejad F. Structural analysis of lipid complexes of GM2-activator protein. J Mol Biol. 2003 Aug 22;331(4):951-64. PMID:12909021
  1. Schroder M, Schnabel D, Suzuki K, Sandhoff K. A mutation in the gene of a glycolipid-binding protein (GM2 activator) that causes GM2-gangliosidosis variant AB. FEBS Lett. 1991 Sep 23;290(1-2):1-3. PMID:1915858
  2. Schroder M, Schnabel D, Hurwitz R, Young E, Suzuki K, Sandhoff K. Molecular genetics of GM2-gangliosidosis AB variant: a novel mutation and expression in BHK cells. Hum Genet. 1993 Nov;92(5):437-40. PMID:8244332
  3. Schepers U, Glombitza G, Lemm T, Hoffmann A, Chabas A, Ozand P, Sandhoff K. Molecular analysis of a GM2-activator deficiency in two patients with GM2-gangliosidosis AB variant. Am J Hum Genet. 1996 Nov;59(5):1048-56. PMID:8900233

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