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Protein

Ras-related protein Rab-39B

Gene

RAB39B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Small GTPases Rab involved in autophagy (PubMed:27103069). 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 sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (PubMed:27103069). May regulate the homeostasis of SNCA/alpha-synuclein. Together with PICK1 proposed to ensure selectively GRIA2 exit from the endoplasmic reticulum to the Golgi and to regulate AMPAR compostion at the post-synapses and thus synaptic transmission (By similarity).By similarity1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi15 – 22GTPBy similarity8
Nucleotide bindingi64 – 68GTPBy similarity5
Nucleotide bindingi123 – 126GTPBy similarity4

GO - Molecular functioni

  • GTPase activity Source: InterPro
  • GTP binding Source: UniProtKB-KW
  • myosin V binding Source: UniProtKB

GO - Biological processi

  • autophagy Source: UniProtKB-KW
  • protein transport Source: UniProtKB-KW
  • regulation of autophagy Source: UniProtKB
  • synapse organization Source: UniProtKB
  • vesicle-mediated transport Source: UniProtKB

Keywordsi

Biological processAutophagy, Protein transport, Transport
LigandGTP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-8873719. RAB geranylgeranylation.
R-HSA-8876198. RAB GEFs exchange GTP for GDP on RABs.

Names & Taxonomyi

Protein namesi
Recommended name:
Ras-related protein Rab-39B
Gene namesi
Name:RAB39B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

EuPathDBiHostDB:ENSG00000155961.4.
HGNCiHGNC:16499. RAB39B.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell membrane, Cytoplasmic vesicle, Golgi apparatus, Membrane

Pathology & Biotechi

Involvement in diseasei

Mental retardation, X-linked 72 (MRX72)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. MRX72 patients can manifest autism spectrum disorder, seizures and macrocephaly as additional features.
See also OMIM:300271
Waisman syndrome (WSMN)3 Publications
The disease is caused by mutations affecting the gene represented in this entry. Its association with Parkinson disease is however unclear (PubMed:26739247, PubMed:27459931). According to a number of studies, variations affecting this gene are not a frequent cause of Parkinson disease, suggesting that RAB39B does not play a major role in Parkinson disease etiology (PubMed:26739247, PubMed:27459931).2 Publications
Disease descriptionA neurologic disorder characterized by delayed psychomotor development, intellectual disability, and early-onset Parkinson disease.
See also OMIM:311510
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073264168T → K in WSMN; loss of function mutation; expression of the mutation in neuroblastoma cells results in low levels of the mutant protein. 1 PublicationCorresponds to variant dbSNP:rs587777874Ensembl.1
Natural variantiVAR_078514186 – 213Missing in WSMN. 1 PublicationAdd BLAST28
Natural variantiVAR_078515192G → R in WSMN; impaired localization to cytoplasmic vesicles. 1 PublicationCorresponds to variant dbSNP:rs864309527Ensembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi22S → N: Dominant negative mutant. 1 Publication1
Mutagenesisi68Q → L: Constitutively active mutant locked in the active GTP-bound form. 1 Publication1

Keywords - Diseasei

Autism spectrum disorder, Disease mutation, Mental retardation, Parkinson disease

Organism-specific databases

DisGeNETi116442.
MalaCardsiRAB39B.
MIMi300271. phenotype.
311510. phenotype.
OpenTargetsiENSG00000155961.
Orphaneti777. X-linked non-syndromic intellectual disability.
PharmGKBiPA34131.

Polymorphism and mutation databases

DMDMi27734447.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001212551 – 213Ras-related protein Rab-39BAdd BLAST213

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei201PhosphoserineBy similarity1
Lipidationi211S-geranylgeranyl cysteineBy similarity1
Modified residuei213Cysteine methyl esterBy similarity1
Lipidationi213S-geranylgeranyl cysteineBy similarity1

Keywords - PTMi

Lipoprotein, Methylation, Phosphoprotein, Prenylation

Proteomic databases

EPDiQ96DA2.
MaxQBiQ96DA2.
PaxDbiQ96DA2.
PeptideAtlasiQ96DA2.
PRIDEiQ96DA2.

PTM databases

iPTMnetiQ96DA2.
PhosphoSitePlusiQ96DA2.

Expressioni

Tissue specificityi

Highly expressed in the brain.1 Publication

Gene expression databases

BgeeiENSG00000155961.
CleanExiHS_RAB39B.
GenevisibleiQ96DA2. HS.

Organism-specific databases

HPAiHPA001114.
HPA042505.

Interactioni

Subunit structurei

Interacts (in GTP-bound form) with PICK1 (via PDZ domain); a PICK1 homodimer may allow simultaneous association of RAB39B and GRIA2 to PICK1 which is involved in GRIA2 trafficking.1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

  • myosin V binding Source: UniProtKB

Protein-protein interaction databases

BioGridi125507. 30 interactors.
IntActiQ96DA2. 4 interactors.
MINTiMINT-4724040.
STRINGi9606.ENSP00000358466.

Structurei

3D structure databases

ProteinModelPortaliQ96DA2.
SMRiQ96DA2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi37 – 45Effector regionBy similarity9

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

eggNOGiKOG0091. Eukaryota.
ENOG410ZQFG. LUCA.
GeneTreeiENSGT00760000118841.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiQ96DA2.
KOiK07925.
OMAiFIETSSR.
OrthoDBiEOG091G0RUB.
PhylomeDBiQ96DA2.
TreeFamiTF300032.

Family and domain databases

InterProiView protein in InterPro
IPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
PfamiView protein in Pfam
PF00071. Ras. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiView protein in PROSITE
PS51419. RAB. 1 hit.

Sequencei

Sequence statusi: Complete.

Q96DA2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEAIWLYQFR LIVIGDSTVG KSCLIRRFTE GRFAQVSDPT VGVDFFSRLV
60 70 80 90 100
EIEPGKRIKL QIWDTAGQER FRSITRAYYR NSVGGLLLFD ITNRRSFQNV
110 120 130 140 150
HEWLEETKVH VQPYQIVFVL VGHKCDLDTQ RQVTRHEAEK LAAAYGMKYI
160 170 180 190 200
ETSARDAINV EKAFTDLTRD IYELVKRGEI TIQEGWEGVK SGFVPNVVHS
210
SEEVVKSERR CLC
Length:213
Mass (Da):24,622
Last modified:December 1, 2001 - v1
Checksum:i2B2C5B35C61FA88E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti57R → T in AAL12244 (PubMed:12438742).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073264168T → K in WSMN; loss of function mutation; expression of the mutation in neuroblastoma cells results in low levels of the mutant protein. 1 PublicationCorresponds to variant dbSNP:rs587777874Ensembl.1
Natural variantiVAR_078514186 – 213Missing in WSMN. 1 PublicationAdd BLAST28
Natural variantiVAR_078515192G → R in WSMN; impaired localization to cytoplasmic vesicles. 1 PublicationCorresponds to variant dbSNP:rs864309527Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY052478 mRNA. Translation: AAL12244.1.
AL834460 mRNA. Translation: CAD39120.1.
AL356738 Genomic DNA. Translation: CAI41468.1.
BC009714 mRNA. Translation: AAH09714.1.
CCDSiCCDS14766.1.
RefSeqiNP_741995.1. NM_171998.3.
UniGeneiHs.632832.

Genome annotation databases

EnsembliENST00000369454; ENSP00000358466; ENSG00000155961.
GeneIDi116442.
KEGGihsa:116442.
UCSCiuc004fne.5. human.

Similar proteinsi

Entry informationi

Entry nameiRB39B_HUMAN
AccessioniPrimary (citable) accession number: Q96DA2
Secondary accession number(s): Q5JT79, Q8NEX3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 10, 2003
Last sequence update: December 1, 2001
Last modified: September 27, 2017
This is version 147 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families