RAB5A_ORYSJ
ID RAB5A_ORYSJ Reviewed; 203 AA.
AC Q0ILQ6; Q2QLR7; Q94IR3; Q9FEV1;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Ras-related protein Rab5A {ECO:0000305};
DE Short=OsRab5A {ECO:0000303|Ref.1};
DE AltName: Full=Protein GLUTELIN PRECURSOR 4 {ECO:0000303|PubMed:21825104};
DE AltName: Full=Protein GLUTELIN PRECURSOR ACCUMULATION 1 {ECO:0000303|PubMed:21105928};
GN Name=RAB5A {ECO:0000303|Ref.1};
GN Synonyms=GLUP4 {ECO:0000303|PubMed:21825104},
GN GPA1 {ECO:0000303|PubMed:21105928};
GN OrderedLocusNames=Os12g0631100 {ECO:0000312|EMBL:BAF30359.1},
GN LOC_Os12g43550 {ECO:0000312|EMBL:ABG22102.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND INDUCTION.
RX DOI=10.1016/S0168-9452(02)00096-1;
RA Wang X.B., Xia M., Chen Q., Wu Z., Wu P.;
RT "Identification of a new small GTP-binding protein gene OsRab5a, genomic
RT organization, and expression pattern analysis during nitrate supply and
RT early nutrient starvation in rice (Oryza sativa L.) root.";
RL Plant Sci. 163:273-280(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Panicle;
RA Liu X.B., Lin H.X., Li F.Q., Liu L.S.;
RT "Molecular cloning and characterization of Osrab5A, a small GTP-binding
RT protein of Oryza sativa.";
RL Submitted (DEC-2000) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [8]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE,
RP AND DISRUPTION PHENOTYPE.
RX PubMed=21105928; DOI=10.1111/j.1365-313x.2010.04370.x;
RA Wang Y., Ren Y., Liu X., Jiang L., Chen L., Han X., Jin M., Liu S., Liu F.,
RA Lv J., Zhou K., Su N., Bao Y., Wan J.;
RT "OsRab5a regulates endomembrane organization and storage protein
RT trafficking in rice endosperm cells.";
RL Plant J. 64:812-824(2010).
RN [9]
RP FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, MUTAGENESIS OF
RP GLY-45, AND ISOPRENYLATION AT CYS-201 AND CYS-202.
RX PubMed=21825104; DOI=10.1104/pp.111.180505;
RA Fukuda M., Satoh-Cruz M., Wen L., Crofts A.J., Sugino A., Washida H.,
RA Okita T.W., Ogawa M., Kawagoe Y., Maeshima M., Kumamaru T.;
RT "The small GTPase Rab5a is essential for intracellular transport of
RT proglutelin from the Golgi apparatus to the protein storage vacuole and
RT endosomal membrane organization in developing rice endosperm.";
RL Plant Physiol. 157:632-644(2011).
RN [10]
RP FUNCTION, INTERACTION WITH VPS9A, AND MUTAGENESIS OF SER-25 AND GLN-70.
RX PubMed=23723154; DOI=10.1093/mp/sst081;
RA Liu F., Ren Y., Wang Y., Peng C., Zhou K., Lv J., Guo X., Zhang X.,
RA Zhong M., Zhao S., Jiang L., Wang H., Bao Y., Wan J.;
RT "OsVPS9A functions cooperatively with OsRAB5A to regulate post-Golgi dense
RT vesicle-mediated storage protein trafficking to the protein storage vacuole
RT in rice endosperm cells.";
RL Mol. Plant 6:1918-1932(2013).
RN [11]
RP INTERACTION WITH VPS9A.
RX PubMed=24488962; DOI=10.1105/tpc.113.121376;
RA Ren Y., Wang Y., Liu F., Zhou K., Ding Y., Zhou F., Wang Y., Liu K.,
RA Gan L., Ma W., Han X., Zhang X., Guo X., Wu F., Cheng Z., Wang J., Lei C.,
RA Lin Q., Jiang L., Wu C., Bao Y., Wang H., Wan J.;
RT "GLUTELIN PRECURSOR ACCUMULATION3 encodes a regulator of post-Golgi
RT vesicular traffic essential for vacuolar protein sorting in rice
RT endosperm.";
RL Plant Cell 26:410-425(2014).
RN [12]
RP FUNCTION, AND INTERACTION WITH NSF AND RBP-L.
RX PubMed=32471860; DOI=10.1105/tpc.20.00111;
RA Tian L., Doroshenk K.A., Zhang L., Fukuda M., Washida H., Kumamaru T.,
RA Okita T.;
RT "Zipcode RNA-binding proteins and membrane trafficking proteins cooperate
RT to transport glutelin mRNAs in rice endosperm.";
RL Plant Cell 32:2566-2581(2020).
CC -!- FUNCTION: Plays an important role in intracellular trafficking of seed
CC storage proteins to the protein storage vacuoles (PSVs)
CC (PubMed:21105928). Participates in the transport of the proglutelins
CC from the Golgi apparatus to the PSVs in endosperm (PubMed:21825104).
CC Functions cooperatively with VPS9A to regulate post-Golgi dense
CC vesicle-mediated transport of storage proteins to the type II protein
CC bodies (PBII) protein storage vacuoles in developing endosperm
CC (PubMed:23723154). Involved in the maintenance of the general
CC structural organization of the endomembrane system in developing
CC endosperm (PubMed:21105928, PubMed:21825104). Binds GTP in vitro
CC (PubMed:21105928, PubMed:21825104, PubMed:23723154). Forms a quaternary
CC complex with the two glutelin zipcode RNA-binding proteins RBP-L and
CC RBP-P, and the membrane trafficking factor NSF (PubMed:32471860). This
CC quaternay complex carries glutelin mRNAs for active transport on
CC endosomes to the cortical endoplasmic reticulum membrane, and enables
CC endosome-mediated glutelin mRNA transport in endosperm cells
CC (PubMed:32471860). {ECO:0000269|PubMed:21105928,
CC ECO:0000269|PubMed:21825104, ECO:0000269|PubMed:23723154,
CC ECO:0000269|PubMed:32471860}.
CC -!- SUBUNIT: Interacts with VPS9A (PubMed:23723154, PubMed:24488962).
CC Interacts with NSF and RBP-L (PubMed:32471860).
CC {ECO:0000269|PubMed:23723154, ECO:0000269|PubMed:24488962,
CC ECO:0000269|PubMed:32471860}.
CC -!- SUBCELLULAR LOCATION: Prevacuolar compartment membrane
CC {ECO:0000269|PubMed:21105928, ECO:0000269|PubMed:21825104}; Lipid-
CC anchor {ECO:0000305}. Golgi apparatus membrane
CC {ECO:0000269|PubMed:21105928, ECO:0000269|PubMed:21825104}; Lipid-
CC anchor {ECO:0000305}. Cell membrane {ECO:0000269|PubMed:21825104};
CC Lipid-anchor {ECO:0000305}. Protein storage vacuole membrane
CC {ECO:0000269|PubMed:21825104}; Lipid-anchor {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Highly expressed in roots (Ref.1). Expressed at low
CC levels in shoots, flowers and grains (Ref.1). {ECO:0000269|Ref.1}.
CC -!- DEVELOPMENTAL STAGE: Expression in developing seeds is low from 6 to 12
CC days after flowering (DAF), peaks at 12 DAF and is barely detected at
CC 15 DAF. {ECO:0000269|PubMed:21105928}.
CC -!- INDUCTION: Induced by nitrogen and phosphorus starvation in roots.
CC {ECO:0000269|Ref.1}.
CC -!- DISRUPTION PHENOTYPE: Accumulation of proglutelins in seed endosperm
CC (PubMed:21105928, PubMed:21825104). Mistargeting of dense vesicles
CC (DVs) to the type II protein bodies (PBII) protein storage vacuoles and
CC reduction of PBII size in endosperm. Formation of paramural bodies
CC (PMBs) secretory vesicle-like structures charged with DVs in endosperm
CC (PubMed:21105928, PubMed:21825104). {ECO:0000269|PubMed:21105928,
CC ECO:0000269|PubMed:21825104}.
CC -!- SIMILARITY: Belongs to the small GTPase superfamily. Rab family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABA99930.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY029301; AAK38149.1; -; mRNA.
DR EMBL; AJ292320; CAC19792.1; -; mRNA.
DR EMBL; DP000011; ABG22102.1; -; Genomic_DNA.
DR EMBL; DP000011; ABA99930.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008218; BAF30359.1; -; Genomic_DNA.
DR EMBL; AP014968; BAT18213.1; -; Genomic_DNA.
DR EMBL; AK061116; BAG87736.1; -; mRNA.
DR RefSeq; XP_015619916.1; XM_015764430.1.
DR AlphaFoldDB; Q0ILQ6; -.
DR SMR; Q0ILQ6; -.
DR STRING; 4530.OS12T0631100-01; -.
DR PRIDE; Q0ILQ6; -.
DR EnsemblPlants; Os12t0631100-01; Os12t0631100-01; Os12g0631100.
DR EnsemblPlants; Os12t0631100-02; Os12t0631100-02; Os12g0631100.
DR GeneID; 4352862; -.
DR Gramene; Os12t0631100-01; Os12t0631100-01; Os12g0631100.
DR Gramene; Os12t0631100-02; Os12t0631100-02; Os12g0631100.
DR KEGG; osa:4352862; -.
DR eggNOG; KOG0092; Eukaryota.
DR HOGENOM; CLU_041217_10_2_1; -.
DR InParanoid; Q0ILQ6; -.
DR OMA; AVHFDIW; -.
DR OrthoDB; 1340129at2759; -.
DR PlantReactome; R-OSA-9626305; Regulatory network of nutrient accumulation.
DR Proteomes; UP000000763; Chromosome 12.
DR Proteomes; UP000059680; Chromosome 12.
DR GO; GO:0030139; C:endocytic vesicle; IBA:GO_Central.
DR GO; GO:0005768; C:endosome; IBA:GO_Central.
DR GO; GO:0000139; C:Golgi membrane; IDA:UniProtKB.
DR GO; GO:0009705; C:plant-type vacuole membrane; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IDA:UniProtKB.
DR GO; GO:0032586; C:protein storage vacuole membrane; IDA:UniProtKB.
DR GO; GO:0005525; F:GTP binding; IDA:UniProtKB.
DR GO; GO:0003924; F:GTPase activity; IBA:GO_Central.
DR GO; GO:0010256; P:endomembrane system organization; IMP:UniProtKB.
DR GO; GO:0006886; P:intracellular protein transport; IMP:UniProtKB.
DR GO; GO:0051028; P:mRNA transport; IDA:UniProtKB.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR InterPro; IPR001806; Small_GTPase.
DR Pfam; PF00071; Ras; 1.
DR SMART; SM00174; RHO; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00231; small_GTP; 1.
DR PROSITE; PS51419; RAB; 1.
PE 1: Evidence at protein level;
KW Cell membrane; Golgi apparatus; GTP-binding; Lipoprotein; Membrane;
KW Nucleotide-binding; Prenylation; Protein transport; Reference proteome;
KW Transport; Vacuole.
FT CHAIN 1..203
FT /note="Ras-related protein Rab5A"
FT /id="PRO_0000445091"
FT MOTIF 40..48
FT /note="Effector region"
FT /evidence="ECO:0000305"
FT BINDING 18..26
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:Q9SN68"
FT BINDING 66..70
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:Q9SN68"
FT BINDING 124..127
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:Q9SN68"
FT BINDING 154..155
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250|UniProtKB:Q9SN68"
FT LIPID 201
FT /note="S-geranylgeranyl cysteine"
FT /evidence="ECO:0000305|PubMed:21825104"
FT LIPID 202
FT /note="S-geranylgeranyl cysteine"
FT /evidence="ECO:0000305|PubMed:21825104"
FT MUTAGEN 25
FT /note="S->N: No effect on the interaction with VPS9A."
FT /evidence="ECO:0000269|PubMed:23723154"
FT MUTAGEN 45
FT /note="G->D: In EM960; Accumulation of proglutelins in
FT seeds and abnormal organization of the endomembrane system
FT in endosperm."
FT /evidence="ECO:0000269|PubMed:21825104"
FT MUTAGEN 70
FT /note="Q->L: Abolishes the interaction with VPS9A."
FT /evidence="ECO:0000269|PubMed:23723154"
FT CONFLICT 75
FT /note="S -> G (in Ref. 1; AAK38149)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 203 AA; 22146 MW; 0C6FED6950BCA92F CRC64;
MAANPGNKIR NAKLVLLGDV GTGKSSLVLR FVKGQFVEFQ ESTIGAAFFS QTLAVNDETV
KFEIWDTAGQ ERYHSLAPMY YRGAAAAIVV YDITNAASFT RAKKWVQELQ AQGNPNTIMA
LAGNKADMVE ARQVPAEEAK TYAQENGLFF METSAKTAIN VNDVFHEIAK RLLQGQQAQD
TPAGMVLNQR PAERMVSSSS CCS
