5qF. View the map and BAC contig (data from UCSC genome browser).
Vps33a (NM_029929): 13 exons, 38,960bp, chr5:122,580,968-122,619,927.
The figure below shows the structure of the Vps33a gene (data from UCSC genome browser).
Search the 5'UTR and 1kb upstream regions (human and mouse) by CONREAL with 80% Position Weight Matrices (PWMs) threshold (view results here).
|Protein||NP_075067 (596aa)||NP_075250 (597aa)||13152 (577aa)||AAD38513 (617aa)||Vps33p |
(1) Domains predicted by SMART:
a) low complexity: 12 - 27
b) low complexity: 225 - 237
(2) Transmembrane domains predicted by SOSUI: none.
(3) CDD domain: KOG1302: Vacuolar sorting protein VPS33/slp1 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport].
(4) Graphic view of InterPro domain structure.
(1) Predicted results by ScanProsite:
a) N-glycosylation site [pattern] [Warning: pattern with a high probability of occurrence]:
355 - 358 NHTS.
b) Tyrosine sulfation site [rule] [Warning: rule with a high probability of occurrence]:
157 - 171 egafkecYlegdqts, 291 - 305 lnsaeelYaeirdkn.
c) Protein kinase C phosphorylation site [pattern] [Warning: pattern with a high probability of occurrence]:
65 - 67 TlK, 314 - 316 SkK, 388 - 390 TdK, 467 - 469 TiR, 471 - 473 TlR, 498 - 500 SvR, 580 - 582 TtK.
(2) Predicted results of subprograms by PSORT II:
a) N-terminal signal peptide: none
b) KDEL ER retention motif in the C-terminus: none
c) ER Membrane Retention Signals: KKXX-like motif in the C-terminus: MEKP
d) VAC possible vacuolar targeting motif: none
e) Actinin-type actin-binding motif: type 1: none; type 2: none
f) Prenylation motif: none
g) memYQRL transport motif from cell surface to Golgi: none
h) Tyrosines in the tail: too long tail
i) Dileucine motif in the tail: found - LL at 54.
(1) ModBase: predicted comparative 3D structures on Q9D2N9 (data from UCSC Gene Sorter). (from left to right: Front, Top, Side view)
(2) 3D models predicted by SPARKS (fold recognition) below. View the models by PDB2MGIF.
This protein does not exist in the current release of SWISS-2DPAGE.
Computed theoretical MW=67,527Da, pI=6.64.
a) Process: Golgi-to-vacuole protein transport, protein secretion (overview of trafficking pathway here).
b) Belongs to the STXBP/UNC-18/SEC1 family.
c) Component of membrane.
Cytoplasmic, peripheral membrane protein associated with late endosomes/lysosomes. Vps33p is an ATP-binding protein that localizes to the cytosol in an energy-dependent manner (Gerhardts, et al; Banta, et al).
This gene is a member of the Sec-1 domain family, and it encodes a protein similar to the yeast class C Vps33 protein. A large hetero-oligomeric class C Vps complex consists of VPS33 together with VPS11, VPS16, VPS18, and probably also the VPS39 and VPS41 proteins (Huizing, et al; Rieder, et al ). In yeast, a 38S complex consisting of both Vam2/6p and the class C Vps proteins, which is termed as HOPS, is responsible for homotypic fusion and vacuole protein sorting (Seals, et al). The C-Vps complex binds to Vam3-Vti1-Vam7 paired SNARE complexes and STX7 (Sato, et al). At the endosome, Vps33p and other class C members exist as a complex with Vps8p, a protein previously known to act in transport between the late Golgi and the endosome. C. elegans SPE-39 interacts in vitro with both VPS33A and VPS33B, whereas RNA interference of VPS33B causes spe-39-like spermatogenesis defects. The human SPE-39 orthologue C14orf133 also interacts with VPS33 homologues and both coimmunoprecipitates and cosediments with other HOPS subunits. SPE-39 knockdown in cultured human cells altered the morphology of syntaxin 7-, syntaxin 8-, and syntaxin 13-positive endosomes (Zhu, et al).
Vps33p also interacts with Pep12p, a known interactor of the SM protein Vps45p (Subramanian, et al). A novel endosomal tethering (CORVET) complex, which interacts with the Rab GTPase Vps21, has been described. Both HOPS and CORVET complexes share the four class C Vps proteins: Vps11, Vps16, Vps18, and Vps33. The HOPS complex, in addition, contains Vps41/Vam2 and Vam6, whereas the CORVET complex has the Vps41 homolog Vps8 and the (h)Vam6 homolog Vps3. The CORVET and HOPS complexes can interconvert which leads to two additional intermediate complexes, both consisting of the class C core bound to Vam6-Vps8 or Vps3-Vps41 (Peplowska, et al). In drosophila, Deep orange and carnation reside in a protein complex that localizes to endosomal compartments (Sevrioukov, et al).
7 proteins are shown to be associated with YLR396C/VPS33 in Yeast GRID.
No entry for the Vps33a drosophila homolog CG12230/car in CuraGen interaction database.
The Class C Vps complex plays essential roles in the processes of membrane docking and fusion at both the Golgi-to-endosome and endosome-to-vacuole stages of transport (view diagram of Class C Vps pathway here). (Peterson, et al; Sato, et al; Pevsner, et al ). Vps33p functions at multiple trafficking steps and is not limited to action at the vacuolar membrane (Subramanian, et al).
SNPs deposited in dbSNP.
|Exon 6||753T>G||753T>G||D251E||missense||bf (B6)||Suzuki, et al|
D251 is highly conserved (refer to the multiple sequence alignment PDF file). This residule is located only three residues distal to the Gly disrupted by the carnation (car) mutation (G249V) in Drosophila. Suzuki, et al further confirmed that the phenotype caused by the D251E mutation was completely complemented by wild-type expression in stably transfected melanocytes.
Mutation in the Vps33a gene is the cause of buff mutant (Suzuki, et al), a mouse model of Hermansky-Pudlak syndrome (OMIM 203300). The bf allele arose from C57BL/6J. On an agouti background, homozygotes have khaki colored coats and show higher than normal levels of lysosomal glycosidases in their kidneys. Melanosomes of the RPE and choroid are reduced in both number and size in the Vps33a/bf mutant (Suzuki, et al). Buff mice showed a novel phenotype observed in urothelial umbrella cells, where the uroplakin-delivering FVs were almost completely replaced by Rab27b-negative multivesicular bodies (MVBs) involved in uroplakin degradation(Guo, et al). In addition, mutation of Vps33a affects the cell surface expression level of RANKL and disrupts the trafficking of RANKL to the secretory lysosomes in osteoblasts or bone marrow stromal cells (BMSCs) (Kariya, et al).
The bf mice demonstrated significant motor deficits (e.g., grip strength, righting reflex and touch escape) worsening with age, progressive Purkinje cell loss, and reduced (~30%) cerebella size (Chintala, et al). The mutant is described in more detail in JAX Mice database (C57BL/6J-Vps33abf/J) and Mouse Locus Card #Vps33a.