1W24

Crystal Structure Of human Vps29

Summary for 1W24

• Entry DOI: 10.2210/pdb1w24/pdb
• Descriptor: VACUOLAR PROTEIN SORTING PROTEIN 29 (2 entities in total)
• Functional Keywords: cytoplasmic protein, vacuolar protein sorting protein, alpha-beta-beta-alpha sandwich
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Cytoplasm: Q9UBQ0
• Total number of polymer chains: 1
• Total formula weight: 20531.71

Authors

Wang, D.,Guo, M.,Teng, M.,Niu, L. (deposition date: 2004-06-26, release date: 2005-03-23, Last modification date: 2024-05-08)

Primary citation

Wang, D.,Guo, M.,Liang, Z.,Fan, J.,Zhu, Z.,Zang, J.,Zhu, Z.,Li, X.,Teng, M.,Niu, L.,Dong, Y.,Liu, P.
Crystal Structure of Human Vacuolar Protein Sorting Protein 29 Reveals a Phosphodiesterase/Nuclease-Like Fold and Two Protein-Protein Interaction Sites.
J.Biol.Chem., 280:22962-, 2005

PubMed Abstract: Vacuolar protein sorting protein 29 (Vps29p), which is involved in retrograde trafficking from prevacuolar endosomes to the trans-Golgi network, performs its biological functions by participating in the formation of a "retromer complex." In human cells, this complex comprises four conserved proteins: hVps35p, hVps29p, hVps26p, and sorting nexin 1 protein (SNX1). Here, we report the crystal structure of hVps29p at 2.1 Angstroms resolution, the first three-dimensional structure of the retromer subunits. This novel structure adopts a four-layered alpha-beta-beta-alpha sandwich fold. hVps29p contains a metal-binding site that is very similar to the active sites of some proteins of the phosphodiesterase/nuclease protein family, indicating that hVps29p may carry out chemically similar functions. Structure and sequence conservation analysis suggests that hVps29p contains two protein-protein interaction sites. One site, which potentially serves as the interface between hVps29p and hVps35p, comprises 5 conserved hydrophobic and 8 hydrophilic residues. The other site is relatively more hydrophilic and may serve as a binding interface with hVps26p, SNX1, or other target proteins.

PubMed: 15788412
DOI: 10.1074/JBC.M500464200

Experimental method

X-RAY DIFFRACTION (2.1 Å)