Palmitoylation summaryValidated by 2 independant techniques or by a targeted study.
High confidence hit in 2 palmitoyl-proteome studies.
7/15human palmitoyl-proteome articles1orthologues in palmitoyl-proteomes0targeted study0orthologue in targeted studies0sitePredicted1cysteines in main isoform
Protein general information
UniProt names and subcellular location Protein identifiers Protein names Subcellular locations Ras-related protein Rab-1B Source Identifiers UniProt gene names RAB1B IPI ID IPI00008964, IPI00896425, IPI00871366 Refseq protein ID NP_112243.1 Ensembl protein ENSP00000310226 Ensembl gene ENSG00000174903 UniProt AC Q9H0U4 UniProt ID RAB1B_HUMAN UniProt secondary AC A8K7S1 Protein length Isoform 1 (main): 201 aa Known functions (from UniProt) The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. RAB1B regulates vesicular transport between the endoplasmic reticulum and successive Golgi compartments. Plays a role in the initial events of the autophagic vacuole development which take place at specialized regions of the endoplasmic reticulum. Rab activation is generally mediated by a guanine exchange factor (GEF), while inactivation through hydrolysis of bound GTP is catalyzed by a GTPase activating protein (GAP). Interacts with MICAL1, MICAL2 and MICAL3. Interacts with GDI1; the interaction requires the GDP-bound state. Interacts with CHM/REP1; the interaction requires the GDP-bound form and is necessary for prenylation by GGTase II. Targeted by REP1 to membranes of specific subcellular compartments including endoplasmic reticulum, Golgi apparatus, and intermediate vesicles between these two compartments. In the GDP-form, colocalizes with GDI in the cytoplasm (By similarity). Prenylated; by GGTase II, only after interaction of the substrate with Rab escort protein 1 (REP1). AMPylation at Tyr-77 by L.pneumophila DrrA occurs in the switch 2 region and leads to moderate inactivation of the GTPase activity. It appears to prolong the lifetime of the GTP state of RAB1B by restricting access of GTPase effectors to switch 2 and blocking effector-stimulated GTP hydrolysis, thereby rendering RAB1B constitutively active. It is later de-AMPylated by L.pneumophila SidD, releasing RAB1B from bacterial phagosomes. Phosphocholinated at Ser-76 by L.pneumophila AnkX, leading to displace GDP dissociation inhibitors (GDI). Both GDP-bound and GTP-bound forms can be phosphocholinated. Dephosphocholinated by L.pneumophila Lem3, restoring accessibility to L.pneumophila GTPase effector LepB. Rab-1B binds GTP and GDP and possesses low intrinsic GTPase activity. Belongs to the small GTPase superfamily. Rab family.
Cysteine summary and predictions
Pos in alignment 23 200 201 Topology U U U Disulfide no no no SS prediction E C C SS UniProt H NA NA Isoform 1
Topology U Undefined E Extracellular/Lumenal T Transmembrane C Cytosolic/Nuclear Prediction scores From top to bottom: Cysteine position, CSS-Palm 4.0 score, PalmPred score
Color code for cysteine position: Predicted (high confidence prediction with CSS-Palm or/and PalmPred) / Predicted but not validated (in terms of disulfide bond and cellular location) / Not predicted
Color code for CSS-Palm 4.0: High confidence, Medium confidence, Low confidence, Not predicted.
Color code for PalmPred: High confidence (score > 0.4), Medium confidence (0.1 > score > 0.4), Low confidence (score < 0.1), Not predicted.
Feature type Isoform 1 phosphorylation 5, 7, 17, 37, 72, 74, 77, 96, 111, 142, 179, 191 ubiquitination 116
UniProt AC UniProt ID Orthology source Organism Gene names Description Isoforms # palmitome articles # targeted studies # of distinct techniques # of known sites Predicted P01123 YPT1_YEAST OMA Yeast YPT1, YP2, YFL038C GTP-binding protein YPT1 (Protein YP2) (Rab GTPase YPT1) (Transport GTPase YPT1) 1 0/1 0 0 0 Yes Q2HJH2 RAB1B_BOVIN MetaPhors Cow RAB1B Ras-related protein Rab-1B 1 0/0 0 0 0 Yes G3V6H0 G3V6H0_RAT OrthoDB, Ensembl Rat LOC100363782, rCG_48149, rCG_63295, LOC102555167, Rab1b Protein LOC100363782 (RCG48149, isoform CRA_b) (RCG63295) 1 0/1 0 0 0 Yes Q9D1G1 RAB1B_MOUSE OrthoDB, Ensembl, InParanoid Mouse Rab1b Ras-related protein Rab-1B 1 2/8 0 2 0 Yes F1PVP9 F1PVP9_CANLF OrthoDB, OMA, Ensembl Dog RAB1B Uncharacterized protein 1 0/0 0 0 0 Yes G3MYN4 G3MYN4_BOVIN OrthoDB, OMA, Ensembl Cow RAB1B Ras-related protein Rab-1B 1 0/0 0 0 0 Yes Q7ZSZ0 Q7ZSZ0_DANRE OrthoDB Zebrafish rab1a, rab1ab RAB1A, member RAS oncogene family (Rab1a protein) (Uncharacterized protein) 1 0/0 0 0 0 Yes O18332 O18332_DROME OrthoDB, InParanoid Fruit fly Rab1, Rab1-RA, CG3320, Dmel_CG3320 FI01544p (Rab1) 1 0/0 0 0 0 Yes Q9SEH3 RAD2C_ARATH OMA Arabidopsis thaliana RABD2C, RAB1C, At4g17530, dl4800c, FCAALL.87 Ras-related protein RABD2c (AtRABD2c) (Ras-related protein Rab1C) (AtRab1C) 1 0/1 0 0 0 Yes Q9FPJ4 RAD2B_ARATH OMA Arabidopsis thaliana RABD2B, RAB1A, At5g47200, MQL5.5 Ras-related protein RABD2b (AtRABD2b) (Ras-related protein Rab1A) (AtRab1A) 1 0/1 0 0 0 Yes P28188 RAD2A_ARATH OMA Arabidopsis thaliana RABD2A, ARA-5, RAB1B, At1g02130, T7I23.6 Ras-related protein RABD2a (AtRABD2a) (Ras-related protein Ara-5) (Ras-related protein Rab1B) (AtRab1B) 1 0/1 0 0 0 Yes Q7K6A8 Q7K6A8_PLAF7 OMA Plasmodium falciparum Rab1b, PFE0625w Rab1b, GTPase 1 0/1 0 0 0 Yes P11620 YPT1_SCHPO OMA Schizosaccharomyces pombe ypt1, SPBC1703.10 GTP-binding protein ypt1 1 0/1 0 0 0 Yes Q0PD66 Q0PD66_MOUSE OMA Mouse Rab1b, Rab1B, mCG_8376 RAB1B, member RAS oncogene family, isoform CRA_c (Rab1B) (Ras-related protein Rab-1B) 1 0/8 0 0 0 Yes F2Z5U4 F2Z5U4_PIG OrthoDB Pig RAB1B Ras-related protein Rab-1B 1 0/0 0 0 0 No Q7ZUV5 Q7ZUV5_DANRE OrthoDB Zebrafish rab1ba, zgc:56049 Uncharacterized protein (Zgc:56049) (Zgc:56049 protein) 1 0/0 0 0 0 Yes O15971 O15971_DROME OrthoDB Fruit fly Rab10, DRab10, CG17060, Dmel_CG17060 LD39986p (Rab10) 1 0/0 0 0 0 Yes
Biological process Cellular component Molecular function GO:2191507 Protein transport
GO:6119962 Virion assembly
GO:5924091 Intracellular protein transport
GO:6119952 Er to golgi vesicle-mediated transport
GO:2191495 Small gtpase mediated signal transduction
GO:6119973 Regulation of autophagic vacuole assembly
GO:5924094 Rab protein signal transduction
GO:5924088 Endoplasmic reticulum membrane
GO:6119972 Pre-autophagosomal structure membrane
GO:5924076 Golgi membrane
GO:6119951 Endoplasmic reticulum-golgi intermediate compartment
GO:3085901 Golgi apparatus
GO:3535990 Extracellular vesicular exosome
GO:3535989 Protein binding
GO:2191474 Gtp binding
GO:5924081 Gtpase activity
Palmitoylation hits and sites
Hit ID Study # Reference Hit list Isoform # Sites (ID, position, characterisation techniques) SPalmH:694 Study 2 List - None SPalmH:19546 Study 8 List - None SPalmH:20947 Study 7 List - None SPalmH:1111 Study 3 HC - None SPalmH:1522 Study 1 LC - None SPalmH:1992 Study 4 HC - None SPalmH:13067 Study 5 List - None SPalmH:17572 Study 6 LC - None
Study # Reference Organism Cell type Subcellular location Technique(s) Palmitome study? Study 1 Yang W et al., 2010 Homo sapiens DU145 Total membrane ABE (Acyl-Biotin Exchange) Yes Study 2 Marin EP et al., 2012 Homo sapiens Umbilical vein blood To be annotated ABE (Acyl-Biotin Exchange) Yes Study 3 Martin BR et al., 2009 Homo sapiens Jurkat Total membrane Labeling of substrate with 17-ODYA (17-octadecynoic acid) Yes Study 4 Wilson JP et al., 2011 Homo sapiens Jurkat Total cell lysate Labeling of substrate with 17-ODYA (17-octadecynoic acid) Yes Study 5 Serwa RA et al., 2015 Homo sapiens RPE-1 Total cell lysate SILAC, Labelling of substrate with 16-HDYA (16-heptadecynoic acid) Yes Study 6 Yang W et al., 2010 Homo sapiens DU145 Non-lipid raft ABE (Acyl-Biotin Exchange) Yes Study 7 Pinner AL et al., 2016 Homo sapiens Brain Total cell lysate ABE (Acyl-Biotin Exchange) Yes Study 8 Hernandez JL et al., 2016 Homo sapiens MCF7 Total cell lysate Labeling of substrate with alk16 Yes