Cocoa (coa, Hps3)

GENOMIC

Mapping

3qA2. View the map and BAC contig (data from UCSC genome browser).

Structure

(assembly 10/03)
Hps3/NM_080634: 17 exons, 38,681 bp, chr3:20,060,835-20,099,515.

The figure shows the structure of the Hps3 gene. (data from UCSC genome browser).

Regulatory Element

Search the 5'UTR and 1kb upstream regions (seq1=human HPS3, seq2=mouse Hps3) by CONREAL with 80% Position Weight Matrices (PWMs) threshold (view results here).

TRANSCRIPT

RefSeq/ORF

Hps3/NM_080634, 3,976 bp, view ORF and the alignment to genomic.

Expression Pattern

Tissue specificity: Ubiquitous.

Affymetrix microarray expression pattern in SymAtlas from GNF is shown below.

PROTEIN

Sequence

Hermansky-Pudlak syndrome 3 protein homolog (NP_542365): 1,002aa, ExPaSy NiceProt view of Swiss-Prot: Q91VB4.
Synonym: Cocoa protein.

Ortholog

Species	Human	Rat	Zebrafish	Drosophila
GeneView	HPS3	LOC310288	ENSDARG00000015749	CG14562
Protein	NP_115759 (1,004aa)	XP_227003 (721aa)	ENSDARP00000018977 (1,001aa)	Q8MZ59 (1,190aa)
Identities	80%/812aa	72%/599aa	45%/465aa	19%/47aa

View multiple sequence alignment (PDF file) by ClustalW and GeneDoc.

Domain

(1) Domains predicted by SMART:
a) low complexity: 537-551
b) ZnF NFX: 553-563

(2) Transmembrane domains predicted by SOSUI: none (predicted as a soluble protein).

Motif/Site

(1) Predicted results by ScanProsite:
a) N-glycosylation site [pattern] [Warning: pattern with a high probability of occurrence]:
83 - 86 NKTI, 240 - 243 NETS, 490 - 493 NTTA, 609 - 612 NHSL, 852 - 855 NYTD.

b)Tyrosine sulfation site [rule] [Warning: rule with a high probability of occurrence]:
68 - 82 ayseagdYlvaieek, 400 - 414 vaheedlYmdttlka, 606 - 620 fyinhslYenldeel, 846 - 860 dsladknYtddllkl.

c) cAMP- and cGMP-dependent protein kinase phosphorylation site [pattern] [Warning: pattern with a high probability of occurrence]:
457 - 460 RReS, 997 - 1000 RKkS.

d) N-myristoylation site [pattern] [Warning: pattern with a high probability of occurrence]:
226 - 231 GSmsSM, 259 - 264 GgeeNT, 345 - 350 GgedSD

e) Tyrosine kinase phosphorylation site [pattern] [Warning: pattern with a high probability of occurrence]:
295 - 303 RfapDissY, 684 - 691 Kmg.DldmY

(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:
XXRR-like motif in the N-terminus: VRLY
KKXX-like motif in the C-terminus: KKSL
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 148.

3D Model

(1) ModBase: none.

(2) 3D models of isoform (a) predicted by SPARKS (fold recognition) below. View the models by PDB2MGIF.

2D-PAGE

This protein does not exist in the current release of SWISS-2DPAGE.
Computed theoretical MW=113,181Da, pI=5.45.

FUNCTION

Ontology

a) Biological process: organelle organization and biogenesis.
b) Component of cytoplasm.

Location

Cytoplasmic.

Interaction

Gautum, et al reported that Hps3, Hps5, and Hps6 proteins regulate vesicle trafficking to lysosome-related organelles at the physiological level as components of the BLOC-2 (biogenesis of lysosome-related organelles complex-2) protein complex. The native molecular mass of BLOC-2 was estimated to be 340 +/- 64 kDa (view diagram of BLOC-2 complex here). BLOC-2 exists in a soluble pool and associates to membranes as a peripheral membrane protein (Di Pietro, et al).

No interactions found in the CuraGen database by searching its drosophila homolog CG14562.

Pathway

Involved in early stages of melanosome biogenesis and maturation (Suzuki, et al ) ( Nguyen, et al ) (view diagram of melanosome blockage here).

MUTATION

Allele or SNP

4 phenotypic alleles described in MGI:2153839.

SNPs deposited in dbSNP.

Distribution

Location	Genomic	cDNA	Protein	Type	Strain	Reference
Exon 8	1420-1441del 22bp	1420-1441del 22bp	S474del 22bp	frame-shift 482X	coa^3J (B10)	Suzuki, et al
Exon 10	2026ins ~5.3kb IAP, 2020-2026dup	2026ins ~5.3kb IAP, 2020-2026dup	L676ins ~5.3kb IAP	gross insertion	coa^6J (C3H/HeJ)	Suzuki, et al
Exon 11	1879A>T	1879A>T	K627X	nonsense	coa^5J (B10)	Suzuki, et al
Intron 14	splicing acceptor -2A>T	2584-2597del 14bp	S862-S866 del 14bp	frame-shift 898X	coa (B10)	Suzuki, et al

(Numbering of genomic and cDNA sequence is based on the start codon of RefSeq NM_080634.)

Effect

All the mutations are predicted as pathological. The Hps3 transcript in coa/coa is almost invisible, although a ~9.5kb transcript was detected in the Northern blot in coa^6J (Suzuki, et al).

PHENOTYPE

Defects in Hps3 are the cause of the cocoa (coa) mutant (Novak, et al), which is characterized by hypopigmentation and platelet dysfunction. The coa mutation arose spontaneously in the C57BL/10J strain. The strain is described in more detail in JAX Mice database (B6.B10-Hps3^coa/J). The coa coat color phenotype is similar to that seen with ruby (Hps6), and coa/coa mice cannot be distinguished from either ru/ru or coa/coa-ru/ru doubly homozygous mutant mice (Gautum, et al). The mutation also causes decreased life span, increased bleeding time accompanied by symptoms of platelet storage pool deficiency (SPD), including decreased platelet serotonin and decreased visibility of dense granules as analyzed by electron microscopy of unfixed platelets. Unlike many other mouse pigment mutations that cause SPD, cocoa does not affect secretion of lysosomal enzymes. Interestingly, ApoE(-/-), HPS3(-/-) doubly mutant mice were shown to be resistant to thrombotic arterial occlusion. This suggests that the reduced platelet dense-granule secretion in coa is associated with marked protection against the development of arterial thrombosis, inflammation, and neointimal hyperplasia after vascular injury(King, et al).