2AG2

Crystal Structure Analysis of GM2-activator protein complexed with Phosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure Analysis of Phosphatidylcholine-GM2-Activator Product Complexes: Evidence for Hydrolase Activity.

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

(2005) Biochemistry 44: 13510-13521

  • DOI: https://doi.org/10.1021/bi050668w
  • Primary Citation of Related Structures:  
    2AF9, 2AG2, 2AG4, 2AG9, 2AGC

  • PubMed 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.


  • Organizational Affiliation

    Department of Pharmacology, X-ray Crystallography Laboratory, University of Virginia, Charlottesville, Virginia 22908-0735, USA. csw2n@virginia.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ganglioside GM2 activator
A, B, C
164Homo sapiensMutation(s): 0 
Gene Names: GM2A
UniProt & NIH Common Fund Data Resources
Find proteins for P17900 (Homo sapiens)
Explore P17900 
Go to UniProtKB:  P17900
PHAROS:  P17900
GTEx:  ENSG00000196743 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LP3
Query on LP3

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B],
V [auth C]
(7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE
C26 H55 N O7 P
IHNKQIMGVNPMTC-RUZDIDTESA-O
OLA
Query on OLA

Download Ideal Coordinates CCD File 
M [auth B],
W [auth C]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CH5
Query on CH5

Download Ideal Coordinates CCD File 
K [auth B],
U [auth C]
2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM
C8 H21 N O6 P
SUHOQUVVVLNYQR-MRVPVSSYSA-O
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A],
T [auth C]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
N [auth B],
X [auth C]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO
Query on DAO

Download Ideal Coordinates CCD File 
O [auth B]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
H [auth A]
I [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
H [auth A],
I [auth A],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C],
Z [auth C]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
S [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.53α = 90
b = 86.19β = 90
c = 120.48γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary