2KVB

Solution structure of CI-MPR domain 5 bound to N-acetylglucosaminyl 6-phosphomethylmannoside

Summary for 2KVB

• Entry DOI: 10.2210/pdb2kvb/pdb
• Related: 2KVA
• NMR Information: BMRB: 16773
• Descriptor: Cation-independent mannose-6-phosphate receptor (1 entity in total)
• Functional Keywords: transport, lysosome, mannose, receptor, sugar binding, glycoprotein, membrane, phosphoprotein, transmembrane, disulfide bond, protein transport
• Biological source: Bos taurus (bovine)
• Total number of polymer chains: 1
• Total formula weight: 16759.34

Authors

Olson, L.J.,Peterson, F.C.,Volkman, B.F.,Dahms, N.M. (deposition date: 2010-03-10, release date: 2010-07-07, Last modification date: 2023-06-14)

Primary citation

Olson, L.J.,Peterson, F.C.,Castonguay, A.,Bohnsack, R.N.,Kudo, M.,Gotschall, R.R.,Canfield, W.M.,Volkman, B.F.,Dahms, N.M.
Structural basis for recognition of phosphodiester-containing lysosomal enzymes by the cation-independent mannose 6-phosphate receptor.
Proc.Natl.Acad.Sci.USA, 107:12493-12498, 2010

PubMed Abstract: Mannose 6-phosphate (Man-6-P)-dependent trafficking is vital for normal development. The biogenesis of lysosomes, a major cellular site of protein, carbohydrate, and lipid catabolism, depends on the 300-kDa cation-independent Man-6-P receptor (CI-MPR) that transports newly synthesized acid hydrolases from the Golgi. The CI-MPR recognizes lysosomal enzymes bearing the Man-6-P modification, which arises by the addition of GlcNAc-1-phosphate to mannose residues and subsequent removal of GlcNAc by the uncovering enzyme (UCE). The CI-MPR also recognizes lysosomal enzymes that elude UCE maturation and instead display the Man-P-GlcNAc phosphodiester. This ability of the CI-MPR to target phosphodiester-containing enzymes ensures lysosomal delivery when UCE activity is deficient. The extracellular region of the CI-MPR is comprised of 15 repetitive domains and contains three distinct Man-6-P binding sites located in domains 3, 5, and 9, with only domain 5 exhibiting a marked preference for phosphodiester-containing lysosomal enzymes. To determine how the CI-MPR recognizes phosphodiesters, the structure of domain 5 was determined by NMR spectroscopy. Although domain 5 contains only three of the four disulfide bonds found in the other seven domains whose structures have been determined to date, it adopts the same fold consisting of a flattened beta-barrel. Structure determination of domain 5 bound to N-acetylglucosaminyl 6-phosphomethylmannoside, along with mutagenesis studies, revealed the residues involved in diester recognition, including Y679. These results show the mechanism by which the CI-MPR recognizes Man-P-GlcNAc-containing ligands and provides new avenues to investigate the role of phosphodiester-containing lysosomal enzymes in the biogenesis of lysosomes.

PubMed: 20615935
DOI: 10.1073/pnas.1004232107

Experimental method

SOLUTION NMR