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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

May be involved in vesicular trafficking. Plays a role in synapse formation. May regulate the homeostasis of SNCA/alpha-synuclein.By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi15 – 228GTPBy similarity
Nucleotide bindingi64 – 685GTPBy similarity
Nucleotide bindingi123 – 1264GTPBy similarity

GO - Molecular functioni

  1. GTPase activity Source: GO_Central
  2. GTP binding Source: UniProtKB-KW
  3. myosin V binding Source: UniProtKB

GO - Biological processi

  1. intracellular protein transport Source: GO_Central
  2. metabolic process Source: GOC
  3. Rab protein signal transduction Source: GO_Central
  4. synapse organization Source: UniProtKB
  5. vesicle-mediated transport Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Keywords - Ligandi

GTP-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Ras-related protein Rab-39B
Gene namesi
Name:RAB39B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:16499. RAB39B.

Subcellular locationi

  1. Cell membrane Curated; Lipid-anchor Curated; Cytoplasmic side Curated
  2. Golgi apparatus 1 Publication

  3. Note: Partial colocalization with markers that cycle from the cell surface to the trans-Golgi network.By similarity

GO - Cellular componenti

  1. Golgi apparatus Source: UniProtKB
  2. intracellular Source: LIFEdb
  3. neuron projection Source: UniProtKB
  4. plasma membrane Source: UniProtKB-SubCell
  5. 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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti168 – 1681T → K in WSMN; loss of function mutation; expression of the mutation in neuroblastoma cells results in low levels of the mutant protein. 1 Publication
VAR_073264

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

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

Polymorphism and mutation databases

DMDMi27734447.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 213213Ras-related protein Rab-39BPRO_0000121255Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi211 – 2111S-geranylgeranyl cysteineBy similarity
Modified residuei213 – 2131Cysteine methyl esterBy similarity
Lipidationi213 – 2131S-geranylgeranyl cysteineBy similarity

Keywords - PTMi

Lipoprotein, Methylation, Prenylation

Proteomic databases

MaxQBiQ96DA2.
PaxDbiQ96DA2.
PeptideAtlasiQ96DA2.
PRIDEiQ96DA2.

PTM databases

PhosphoSiteiQ96DA2.

Expressioni

Tissue specificityi

Highly expressed in the brain.1 Publication

Gene expression databases

BgeeiQ96DA2.
CleanExiHS_RAB39B.
GenevestigatoriQ96DA2.

Organism-specific databases

HPAiHPA001114.
HPA042505.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi125507. 16 interactions.
IntActiQ96DA2. 3 interactions.
MINTiMINT-4724040.
STRINGi9606.ENSP00000358466.

Structurei

3D structure databases

ProteinModelPortaliQ96DA2.
SMRiQ96DA2. Positions 7-171.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi37 – 459Effector regionBy similarity

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

eggNOGiCOG1100.
GeneTreeiENSGT00760000118841.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiQ96DA2.
KOiK07925.
OMAiTKSDRRC.
OrthoDBiEOG7JHM6Q.
PhylomeDBiQ96DA2.
TreeFamiTF300032.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
PRINTSiPR00449. RASTRNSFRMNG.
SMARTiSM00175. RAB. 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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti57 – 571R → T in AAL12244 (PubMed:12438742).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti168 – 1681T → K in WSMN; loss of function mutation; expression of the mutation in neuroblastoma cells results in low levels of the mutant protein. 1 Publication
VAR_073264

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.3. 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. Positions 7-171.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125507. 16 interactions.
IntActiQ96DA2. 3 interactions.
MINTiMINT-4724040.
STRINGi9606.ENSP00000358466.

PTM databases

PhosphoSiteiQ96DA2.

Polymorphism and mutation databases

DMDMi27734447.

Proteomic databases

MaxQBiQ96DA2.
PaxDbiQ96DA2.
PeptideAtlasiQ96DA2.
PRIDEiQ96DA2.

Protocols and materials databases

DNASUi116442.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000369454; ENSP00000358466; ENSG00000155961.
GeneIDi116442.
KEGGihsa:116442.
UCSCiuc004fne.3. human.

Organism-specific databases

CTDi116442.
GeneCardsiGC0XM154487.
HGNCiHGNC:16499. RAB39B.
HPAiHPA001114.
HPA042505.
MIMi300271. phenotype.
300774. gene.
311510. phenotype.
neXtProtiNX_Q96DA2.
Orphaneti777. X-linked non-syndromic intellectual disability.
PharmGKBiPA34131.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1100.
GeneTreeiENSGT00760000118841.
HOGENOMiHOG000233968.
HOVERGENiHBG009351.
InParanoidiQ96DA2.
KOiK07925.
OMAiTKSDRRC.
OrthoDBiEOG7JHM6Q.
PhylomeDBiQ96DA2.
TreeFamiTF300032.

Miscellaneous databases

GeneWikiiRAB39B.
GenomeRNAii116442.
NextBioi79915.
PROiQ96DA2.
SOURCEiSearch...

Gene expression databases

BgeeiQ96DA2.
CleanExiHS_RAB39B.
GenevestigatoriQ96DA2.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]
PfamiPF00071. Ras. 1 hit.
[Graphical view]
PRINTSiPR00449. RASTRNSFRMNG.
SMARTiSM00175. RAB. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and characterization of a human novel RAB (RAB39B) gene."
    Cheng H., Ma Y., Ni X., Jiang M., Guo L., Ying K., Xie Y., Mao Y.
    Cytogenet. Genome Res. 97:72-75(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Fetal brain.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  3. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Pancreas.
  5. Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INVOLVEMENT IN MRX72.
  6. Cited for: INVOLVEMENT IN WSMN, VARIANT WSMN LYS-168, CHARACTERIZATION OF VARIANT WSMN LYS-168.

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: April 29, 2015
This is version 124 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

External Data

Dasty 3

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 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.