Structural basis of sterol binding by NPC2, a lysosomal protein deficient in Niemann-Pick type C2 disease.
NPC2 is a small lysosomal glycoprotein that binds cholesterol with submicromolar affinity. Deficiency in NPC2 is the cause of Niemann-Pick type C2 disease, a fatal neurovisceral disorder characterized by accumulation of cholesterol in lysosomes. Here we report the crystal structure of bovine NPC2 bound to cholesterol-3-O-sulfate, an analog that binds with greater apparent affinity than cholesterol. Structures of both apo-bound and sterol-bound NPC2 were observed within the same crystal lattice, with an asymmetric unit containing one molecule of apoNPC2 and two molecules of sterol-bound NPC2. As predicted from a previously determined structure of apoNPC2, the sterol binds in a deep hydrophobic pocket sandwiched between the two beta-sheets of NPC2, with only the sulfate substituent of the ligand exposed to solvent. In the two available structures of apoNPC2, the incipient ligand-binding pocket, which ranges from a loosely packed hydrophobic core to a small tunnel, is too small to accommodate cholesterol. In the presence of sterol, the pocket expands, facilitated by a slight separation of the beta-strands and substantial reorientation of some side chains, resulting in a perfect molding of the pocket around the hydrocarbon portion of cholesterol. A notable feature is the repositioning of two aromatic residues at the tunnel entrance that are essential for NPC2 function. The NPC2 structures provide evidence of a malleable binding site, consistent with the previously documented broad range of sterol ligand specificity.
Xu
Sujuan
S
Center for Advanced Biotechnology and Medicine, Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
Benoff
Brian
B
Liou
Heng-Ling
HL
Lobel
Peter
P
Stock
Ann M
AM
D000818:Animals; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry*; D002417:Cattle; D002784:Cholesterol / Q000378:metabolism; D002788:Cholesterol Esters / Q000737:chemistry*; D018360:Crystallography, X-Ray; D006023:Glycoproteins / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D008247:Lysosomes / Q000378:metabolism*; D008954:Models, Biological; D052556:Niemann-Pick Disease, Type C / Q000378:metabolism*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013261:Sterols / Q000737:chemistry; D033921:Vesicular Transport Proteins
D002352:Carrier Proteins; D002788:Cholesterol Esters; D006023:Glycoproteins; D008024:Ligands; C104585:NPC2 protein, human; D013261:Sterols; D033921:Vesicular Transport Proteins; D002784:Cholesterol; C007045:cholesteryl sulfate