RABGGTA

GENOMIC

Mapping

14q11.2 View the map and BAC clones of FISH (data from UCSC genome browser).

Structure

(assembly 07/03)
Isoform a (NM_182836): 17 exons, 6,058bp, Chr14: 22,724,874 - 22,730,931.
Isoform b (NM_004581): 16 exons, 6,058bp, Chr14: 22,724,874 - 22,730,931.

Note that NM_004581 differs from NM_182836 in the alternative splicing of exon 1, which leads to a shorter C-terminus. The exon/intron structural organization of the 5'-untranslated region (UTR) of human RABGGTA was found to be similar to that of the mouse Rabggta gene. 5'RACE shows variable 5' ends (Li, et al). van Bokhoven, et al found that the 3' end of the RABGGTA cDNA sequence overlaps the promoter region of TGM1.

The figure below shows the structure of the known isoforms (data from UCSC genome browser).

Regulatory Element

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

Features of the 5'-UTR of RABGGTA suggest it is a housekeeping gene (Li, et al).

TRANSCRIPT

RefSeq/ORF

a) Transcript variant 1 (NM_182836), 1,961bp, view ORF and the alignment to genomic.
a) Transcript variant 2 (NM_004581), 2,280bp, view ORF and the alignment to genomic.

Expression Pattern

Tissue specificity: ubiquitously expressed.

BMR: Bone marrow; SPL: Spleen; TMS: Thymus; BRN: Brain; SPC: Spinal cord; HRT: Heart; MSL: Skeletal muscle; LVR; Liver; PNC: Pancreas; PST: Prostate; KDN: Kidney; LNG: Lung. (data from GeneCards )

PROTEIN

Sequence

(Rab GGTase alpha)
Isoform a (NP_878256): 567aa, ExPaSy NiceProt view of Swiss-Prot:Q92696.
Isoform b (NP_004572): 297aa (encoded by transcript variant 2).
Synonyms: Geranylgeranyl transferase type II alpha subunit; Rab geranylgeranyltransferase alpha subunit; Rab GG transferase alpha.

Ortholog

Species	Mouse	Rat	Zebrafish	Worm
GeneView	gm/Rabggta	LOC58983	19427	M57.2
Protein	NP_062392 (567aa)	NP_113842 (567aa)	7197 (333aa)	CE19541 (580aa)
Identities	90%/515aa	91%/518aa	55%/186aa	30%/182aa
Species	Mosquito	Fruitfly	Yeast
GeneView	1279131	CG12007	YJL031C
Protein	XP_318802 (495aa)	Q9VN77 (515aa)	YJL031C (327aa)
Identities	39%/190aa	37%/176aa	31%/86aa

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

Domain

(1) Domains predicted by SMART:
a) Pfam:PPTA repeats: 47 - 77; 91 - 121; 127 - 157; 162 - 192; 210-240.
b) Pfam:LRR: 462 - 485, 507 - 533.

(2) Graphical view of InterPro domain structure.

(3) Transmembrane domains predicted by SOSUI: none.

(4) CDD domains:
a) COG5536: Protein prenyltransferase, alpha subunit (post-translational modification).
b) COG0529: Protein geranylgeranyltransferase type II, alpha subunit (post-translational modification).

Motif/Site

(1) Predicted results by ScanProsite:
a) Leucine-rich region profile : [occurs frequently]
385 - 559: score=10.339

b) Protein kinase C phosphorylation site : [occurs frequently]
78 - 80: TqK, 317 - 319: TfR, 370 - 372: ScK 410 - 412: TlK.

c) N-glycosylation site : [occurs frequently]
124 - 127: NWTR, 174 - 177: NFSN, 177 - 180: NYSS

d) Tyrosine kinase phosphorylation site : [occurs frequently]
393 - 400: RalDpllY

e) Leucine zipper pattern : [occurs frequently]
538 - 559: LnlqgnpLcqavgiLeqlaelL, 545 - 566: LcqavgiLeqlaelLpsvssvL

f) N-myristoylation site : [occurs frequently]
542 - 547: GNplCQ

(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: HGRL
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: none
i) Dileucine motif in the tail: none

3D Model

ModBase (Q92696): predicted comparative 3D structures (data from UCSC Genome Sorter).
From left to right: Front, Top, and Side views of predicted protein.

Front Top Side

2D-PAGE

This protein does not exist in the current release of SWISS-2DPAGE.
Computed theoretical MW=65,072Da, pI=5.45 (NP_878256, isoform a).
Computed theoretical MW=33,767Da, pI=5.02 (NP_004572, isoform b).

FUNCTION

Ontology

a) Process: protein amino acid prenylation.
b) Function: protein prenyltransferase activity.

Location

Cytoplasmic.

Interaction

The RABGGTA gene encode the geranylgeranyl transferase type II alpha subunit (EC 2.5.1.60) (Rab geranylgeranyltransferase alpha subunit, or RabGGTase alpha). RabGGTase catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to both cysteines in Rab proteins with an -XXCC, -XCXC and -CCXX C-terminal, such as RAB1A, RAB3A, RAB5A, and RAB27A respectively. The enzymatic reaction requires the aid of a Rab escort protein (REP, also called component A). Heterodimer of an alpha and a beta subunit, is collectively called component B. The head-to-tail arrangement with the transglutaminase 1 (TGM1) gene does not show that these two genes are functionally related in the terminal differentiation program of epidermal keratinocytes (Song, et al).

2 proteins are shown to be associated with YJL031C/BET4 in Yeast GRID.

Rabggta drosophila homolog CG12007 interaction information in CuraGen interaction database.

Pathway

The enzyme RabGGTase covalently attaches the geranylgeranyl groups to two C-terminal cysteines of the Rab protein. NiceZyme View of protein geranylgeranyltransferase type II within ENZYME: EC 2.5.1.60. More details in BRENDA: RabGGTase.

MUTATION

Allele or SNP

Li, et al performed mutation screening of the human RABGGTA gene in 8 patients with deficiencies of platelet-dense granules (alphadelta-SPD), alpha granules (alpha-SPD or gray platelet syndrome, GPS) or alpha plus dense granules (alphadelta-SPD). Obvious disease-causing mutations of human RABGGTA were not found in these SPD patients by sequencing its entire coding region.

SNPs deposited in dbSNP.

Distribution

(none)

Effect