Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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

May be involved in vesicular trafficking. Plays a role in synapse formation. 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 similarity

Regions

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

GO - Molecular functioni

  • GTP binding Source: UniProtKB-KW
  • myosin V binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000155961-MONOMER.
ReactomeiR-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

HGNCiHGNC:16499. RAB39B.

Subcellular locationi

GO - Cellular componenti

  • Golgi apparatus Source: UniProtKB
  • intracellular Source: LIFEdb
  • neuron projection Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
  • vesicle Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, 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)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
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 rs587777874dbSNPEnsembl.1

Keywords - Diseasei

Autism spectrum disorder, Disease mutation, Mental retardation

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

WithEntry#Exp.IntActNotes
GOLGA2Q083793EBI-9089467,EBI-618309
RUFY1Q96T513EBI-9089467,EBI-3941207
ZDHHC17Q8IUH53EBI-9089467,EBI-524753

GO - Molecular functioni

  • myosin V binding Source: UniProtKB

Protein-protein interaction databases

BioGridi125507. 23 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.
OMAiVNAGGHR.
OrthoDBiEOG091G0RUB.
PhylomeDBiQ96DA2.
TreeFamiTF300032.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]

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 rs587777874dbSNPEnsembl.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.

Cross-referencesi

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.

3D structure databases

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

Protein-protein interaction databases

BioGridi125507. 23 interactors.
IntActiQ96DA2. 4 interactors.
MINTiMINT-4724040.
STRINGi9606.ENSP00000358466.

PTM databases

iPTMnetiQ96DA2.
PhosphoSitePlusiQ96DA2.

Polymorphism and mutation databases

DMDMi27734447.

Proteomic databases

EPDiQ96DA2.
MaxQBiQ96DA2.
PaxDbiQ96DA2.
PeptideAtlasiQ96DA2.
PRIDEiQ96DA2.

Protocols and materials databases

DNASUi116442.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi116442.
DisGeNETi116442.
GeneCardsiRAB39B.
HGNCiHGNC:16499. RAB39B.
HPAiHPA001114.
HPA042505.
MalaCardsiRAB39B.
MIMi300271. phenotype.
300774. gene.
311510. phenotype.
neXtProtiNX_Q96DA2.
OpenTargetsiENSG00000155961.
Orphaneti777. X-linked non-syndromic intellectual disability.
PharmGKBiPA34131.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000155961-MONOMER.
ReactomeiR-HSA-8876198. RAB GEFs exchange GTP for GDP on RABs.

Miscellaneous databases

GeneWikiiRAB39B.
GenomeRNAii116442.
PROiQ96DA2.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000155961.
CleanExiHS_RAB39B.
GenevisibleiQ96DA2. HS.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRB39B_HUMAN
AccessioniPrimary (citable) accession number: Q96DA2
Secondary accession number(s): Q5JT79, Q8NEX3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2003
Last sequence update: December 1, 2001
Last modified: November 30, 2016
This is version 140 of the entry and version 1 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.