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Q8I4E2

- LST4_CAEEL

UniProt

Q8I4E2 - LST4_CAEEL

Protein

Sorting nexin lst-4

Gene

lst-4

Organism
Caenorhabditis elegans
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 1 (01 Mar 2003)
      Previous versions | rss
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    Functioni

    Involved in the signaling of vulval development by acting as a negative regulator of epidermal growth factor receptor (EGFR) signaling. Aids in phagosomal membrane tubule formation which is required for phagosomal fusion with endosomes and lysosomes. Also recruits rab-7 to phagosomes by an intereaction with dyn-1. These are events leading to phagosome maturation which is a step in apoptotic cell corpse clearance. Binds phosphatidylinositol-3,4,5-trisphosphate.4 Publications

    GO - Molecular functioni

    1. GTPase binding Source: WormBase
    2. phosphatidylinositol-3,4,5-trisphosphate binding Source: WormBase
    3. protein binding Source: IntAct
    4. protein self-association Source: WormBase

    GO - Biological processi

    1. intracellular protein transport Source: InterPro
    2. mitotic nuclear division Source: InterPro
    3. phagosome-lysosome fusion involved in apoptotic cell clearance Source: WormBase
    4. phagosome maturation involved in apoptotic cell clearance Source: WormBase

    Keywords - Ligandi

    Lipid-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sorting nexin lst-4By similarity
    Alternative name(s):
    Lateral signaling target protein 42 Publications
    Gene namesi
    Name:lst-4Imported
    ORF Names:Y37A1B.2
    OrganismiCaenorhabditis elegans
    Taxonomic identifieri6239 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
    ProteomesiUP000001940: Chromosome IV

    Organism-specific databases

    WormBaseiY37A1B.2a; CE19071; WBGene00003086; lst-4.
    Y37A1B.2b; CE32245; WBGene00003086; lst-4.
    Y37A1B.2c; CE32246; WBGene00003086; lst-4.
    Y37A1B.2d; CE32247; WBGene00003086; lst-4.
    Y37A1B.2e; CE44602; WBGene00003086; lst-4.
    Y37A1B.2f; CE47745; WBGene00003086; lst-4.

    Subcellular locationi

    Cytoplasm 3 Publications. Cytoplasmic vesiclephagosome membrane 3 Publications
    Note: Recruited to phagosomal surface by phosphatidylinositol trisphosphate. BAR and PX domains are required for the phagosomal localization.3 Publications

    GO - Cellular componenti

    1. cytoplasm Source: WormBase
    2. phagocytic vesicle Source: WormBase
    3. phagocytic vesicle membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Cytoplasmic vesicle, Membrane

    Pathology & Biotechi

    Disruption phenotypei

    Aberrant vulval development, ectopic vulval induction, retained cell corpses and defective recruitment of dyn-1 and rab-7 to phagosomal surfaces.3 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi265 – 2673RYK → QAA: Defective recruitment to the phagosome. 2 Publications
    Mutagenesisi265 – 2651R → Q: Defect recruitment by phosphoinositide to phagosomal surface. 2 Publications
    Mutagenesisi494 – 4941K → E: Defective recruitment to the phagosome. 2 Publications
    Mutagenesisi501 – 5011R → E: Defective recruitment to the phagosome. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 566566Sorting nexin lst-4PRO_0000422772Add
    BLAST

    Proteomic databases

    PRIDEiQ8I4E2.

    Expressioni

    Tissue specificityi

    Expressed in vulval precursor cells (VPCs) and apoptotic germ cells. Colocalizes with actin, dyn-1 and rab-5 in early phagosomes.2 Publications

    Developmental stagei

    Highly expressed in all 6 vulval precursor cells (VPCs). At the time of inductive signaling, expression forms a gradient in response to inductive signal: expression is low in P6.p, intermediate in P5.p and P7.p and undiminished in P3.p, P4.p, and P8.p. Later, expression becomes strong again in P5.p and P7.p.1 Publication

    Interactioni

    Subunit structurei

    Homodimer. Isoform d interacts (via SH3 domain) with dyn-1.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    dyn-1P390554EBI-4325777,EBI-317945

    Protein-protein interaction databases

    IntActiQ8I4E2. 6 interactions.
    STRINGi6239.Y37A1B.2b.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8I4E2.
    SMRiQ8I4E2. Positions 7-56, 190-566.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 6161SH3PROSITE-ProRule annotationAdd
    BLAST
    Domaini227 – 339113PXPROSITE-ProRule annotationAdd
    BLAST
    Domaini362 – 566205BARSequence AnalysisAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi64 – 11552Pro-richSequence AnalysisAdd
    BLAST

    Domaini

    The BAR and PX domains are required for recruitment to the phagosome.1 Publication
    The SH3 domain is involved in phagosome maturation.1 Publication

    Sequence similaritiesi

    Belongs to the sorting nexin family.Sequence Analysis
    Contains 1 BAR domain.Sequence Analysis
    Contains 1 PX (phox homology) domain.PROSITE-ProRule annotation
    Contains 1 SH3 domain.PROSITE-ProRule annotation

    Keywords - Domaini

    SH3 domain

    Phylogenomic databases

    GeneTreeiENSGT00510000046469.
    HOGENOMiHOG000261633.
    KOiK17923.
    OMAiSAIYLEI.

    Family and domain databases

    Gene3Di3.30.1520.10. 1 hit.
    InterProiIPR028650. Lst-4.
    IPR001683. Phox.
    IPR001452. SH3_domain.
    IPR014536. Snx9_subfam.
    IPR019497. Sorting_nexin_WASP-bd-dom.
    [Graphical view]
    PANTHERiPTHR10555:SF11. PTHR10555:SF11. 1 hit.
    PfamiPF10456. BAR_3_WASP_bdg. 1 hit.
    PF00787. PX. 1 hit.
    PF14604. SH3_9. 1 hit.
    [Graphical view]
    PIRSFiPIRSF027744. Snx9. 1 hit.
    PRINTSiPR00452. SH3DOMAIN.
    SMARTiSM00312. PX. 1 hit.
    SM00326. SH3. 1 hit.
    [Graphical view]
    SUPFAMiSSF50044. SSF50044. 1 hit.
    SSF64268. SSF64268. 1 hit.
    PROSITEiPS50195. PX. 1 hit.
    PS50002. SH3. 1 hit.
    [Graphical view]

    Sequences (6)i

    Sequence statusi: Complete.

    This entry describes 6 isoformsi produced by alternative splicing. Align

    Isoform c1 Publication (identifier: Q8I4E2-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MAQVKAEYDF QSQPNTGELS ISAGEVLTVI RENIDGGWIE GRNVRGSVGL    50
    FPESYVTPYQ ASRPPPVLPP PLPPTSSGPP AASSRPFDDW GGASEVAAPP 100
    SYGAQHHHQP TPSVPEVTRS SYPSQNDDFD DEWTDEDDEQ EPTRPNVQSS 150
    IGSNSRRDLS RSHSEHGGPD RGSNKVNKNI NRFSNFVKSG VEAYVIGESK 200
    TTSQISERHE VVMNNGIIQW KPIQQYYTCI VDKPKKESKL KGLKSFIAYS 250
    ITSSLTNIQR QVSRRYKHFD WLHEQLSAKY VLIPIPPLPE KQVAGRYEED 300
    LIDHRKHILQ LWVNKICRHP VLSQSEVWLH FISCTDEKDW KNGKRRAEKD 350
    EYIGGAFLNC ITVPHQPLDP NNVDMQVERF QRSVKTSEEA MRVMQERMNM 400
    FQKVFAGPVK QNWQKMGSAF KTLQQSFEID ETVASRRLTE ALAYTASEYH 450
    EIGQVFDAHT KNDMEPVLEN LYSYKGTVQN VPDIIQVHKQ AVQKFRDSEG 500
    RLSSAEAEKM KQRIDAMSYT VIAEVQHQTA EKVEDMKSTM GTYLKKQAMF 550
    YQEVATKLTS LAARYD 566

    Note: No experimental confirmation available.Curated

    Length:566
    Mass (Da):64,329
    Last modified:March 1, 2003 - v1
    Checksum:i77CFBE901A3E3B24
    GO
    Isoform a1 Publication (identifier: Q8I4E2-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         141-163: EPTRPNVQSSIGSNSRRDLSRSH → VFLKFYFNFLIVQFLSVLFIPSN
         165-566: Missing.

    Note: No experimental confirmation available.Curated

    Show »
    Length:164
    Mass (Da):18,014
    Checksum:i090A42146AAC080C
    GO
    Isoform b1 Publication (identifier: Q8I4E2-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-66: MAQVKAEYDF...TPYQASRPPP → MLFTSSLRKA...FKKSGAISKS

    Note: No experimental confirmation available.Curated

    Show »
    Length:592
    Mass (Da):67,553
    Checksum:i156B568888CD5E78
    GO
    Isoform d1 Publication (identifier: Q8I4E2-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         260-261: Missing.

    Note: No experimental confirmation available.Curated

    Show »
    Length:564
    Mass (Da):64,045
    Checksum:i224A0F3052A1CA3D
    GO
    Isoform e1 Publication (identifier: Q8I4E2-5) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-509: Missing.

    Note: No experimental confirmation available.Curated

    Show »
    Length:57
    Mass (Da):6,580
    Checksum:i5AE1F0267B8630F8
    GO
    Isoform f1 Publication (identifier: Q8I4E2-6) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         2-79: AQVKAEYDFQ...PPLPPTSSGP → STDDETRSSQ...SNRSHHDQNK
         80-140: Missing.

    Note: No experimental confirmation available.Curated

    Show »
    Length:505
    Mass (Da):58,155
    Checksum:i1514E1BFE36F43FE
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 509509Missing in isoform e. 1 PublicationVSP_046628Add
    BLAST
    Alternative sequencei1 – 6666MAQVK…SRPPP → MLFTSSLRKAVENYPTPPGG SSEDAHRQLLERRRKQMLRR HTCSTLIKQDTSASPHKMKP PILMEEEDEQHSTGKHSSRK SSFKKSGAISKS in isoform b. 1 PublicationVSP_046629Add
    BLAST
    Alternative sequencei2 – 7978AQVKA…TSSGP → STDDETRSSQQDGAYPSSKR NGSVGSSTRSTSTKKRLSRQ DSTARRRRLSEERDSRRRVE KSVSSCLSSNRSHHDQNK in isoform f. 1 PublicationVSP_046630Add
    BLAST
    Alternative sequencei80 – 14061Missing in isoform f. 1 PublicationVSP_046631Add
    BLAST
    Alternative sequencei141 – 16323EPTRP…LSRSH → VFLKFYFNFLIVQFLSVLFI PSN in isoform a. 1 PublicationVSP_046632Add
    BLAST
    Alternative sequencei165 – 566402Missing in isoform a. 1 PublicationVSP_046633Add
    BLAST
    Alternative sequencei260 – 2612Missing in isoform d. 1 PublicationVSP_046634

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL023835 Genomic DNA. Translation: CAA19486.1.
    AL023835 Genomic DNA. Translation: CAA19487.2.
    AL023835 Genomic DNA. Translation: CAD56253.1.
    AL023835 Genomic DNA. Translation: CAD56254.1.
    AL023835 Genomic DNA. Translation: CBK19491.1.
    AL023835 Genomic DNA. Translation: CCM09420.1.
    RefSeqiNP_001255779.1. NM_001268850.1. [Q8I4E2-5]
    NP_001263811.1. NM_001276882.1. [Q8I4E2-6]
    NP_502693.2. NM_070292.4. [Q8I4E2-1]
    NP_502694.1. NM_070293.5. [Q8I4E2-2]
    NP_502695.2. NM_070294.4. [Q8I4E2-3]
    NP_872090.1. NM_182290.3. [Q8I4E2-4]
    UniGeneiCel.22885.

    Genome annotation databases

    EnsemblMetazoaiY37A1B.2c; Y37A1B.2c; WBGene00003086. [Q8I4E2-1]
    GeneIDi178361.
    KEGGicel:CELE_Y37A1B.2.
    UCSCiY37A1B.2b. c. elegans. [Q8I4E2-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL023835 Genomic DNA. Translation: CAA19486.1 .
    AL023835 Genomic DNA. Translation: CAA19487.2 .
    AL023835 Genomic DNA. Translation: CAD56253.1 .
    AL023835 Genomic DNA. Translation: CAD56254.1 .
    AL023835 Genomic DNA. Translation: CBK19491.1 .
    AL023835 Genomic DNA. Translation: CCM09420.1 .
    RefSeqi NP_001255779.1. NM_001268850.1. [Q8I4E2-5 ]
    NP_001263811.1. NM_001276882.1. [Q8I4E2-6 ]
    NP_502693.2. NM_070292.4. [Q8I4E2-1 ]
    NP_502694.1. NM_070293.5. [Q8I4E2-2 ]
    NP_502695.2. NM_070294.4. [Q8I4E2-3 ]
    NP_872090.1. NM_182290.3. [Q8I4E2-4 ]
    UniGenei Cel.22885.

    3D structure databases

    ProteinModelPortali Q8I4E2.
    SMRi Q8I4E2. Positions 7-56, 190-566.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q8I4E2. 6 interactions.
    STRINGi 6239.Y37A1B.2b.

    Proteomic databases

    PRIDEi Q8I4E2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblMetazoai Y37A1B.2c ; Y37A1B.2c ; WBGene00003086 . [Q8I4E2-1 ]
    GeneIDi 178361.
    KEGGi cel:CELE_Y37A1B.2.
    UCSCi Y37A1B.2b. c. elegans. [Q8I4E2-1 ]

    Organism-specific databases

    CTDi 178361.
    WormBasei Y37A1B.2a ; CE19071 ; WBGene00003086 ; lst-4.
    Y37A1B.2b ; CE32245 ; WBGene00003086 ; lst-4.
    Y37A1B.2c ; CE32246 ; WBGene00003086 ; lst-4.
    Y37A1B.2d ; CE32247 ; WBGene00003086 ; lst-4.
    Y37A1B.2e ; CE44602 ; WBGene00003086 ; lst-4.
    Y37A1B.2f ; CE47745 ; WBGene00003086 ; lst-4.

    Phylogenomic databases

    GeneTreei ENSGT00510000046469.
    HOGENOMi HOG000261633.
    KOi K17923.
    OMAi SAIYLEI.

    Miscellaneous databases

    NextBioi 900810.

    Family and domain databases

    Gene3Di 3.30.1520.10. 1 hit.
    InterProi IPR028650. Lst-4.
    IPR001683. Phox.
    IPR001452. SH3_domain.
    IPR014536. Snx9_subfam.
    IPR019497. Sorting_nexin_WASP-bd-dom.
    [Graphical view ]
    PANTHERi PTHR10555:SF11. PTHR10555:SF11. 1 hit.
    Pfami PF10456. BAR_3_WASP_bdg. 1 hit.
    PF00787. PX. 1 hit.
    PF14604. SH3_9. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF027744. Snx9. 1 hit.
    PRINTSi PR00452. SH3DOMAIN.
    SMARTi SM00312. PX. 1 hit.
    SM00326. SH3. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50044. SSF50044. 1 hit.
    SSF64268. SSF64268. 1 hit.
    PROSITEi PS50195. PX. 1 hit.
    PS50002. SH3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
      The C. elegans sequencing consortium
      Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
      Strain: Bristol N2Imported.
    2. "Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development."
      Yoo A.S., Bais C., Greenwald I.
      Science 303:663-666(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
    3. Cited for: FUNCTION.
    4. "Three sorting nexins drive the degradation of apoptotic cells in response to PtdIns(3)P signaling."
      Lu N., Shen Q., Mahoney T.R., Liu X., Zhou Z.
      Mol. Biol. Cell 22:354-374(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH DYN-1, DOMAIN, DISRUPTION PHENOTYPE, MUTAGENESIS OF ARG-265; LYS-494 AND ARG-501.
    5. "A conserved role for SNX9-family members in the regulation of phagosome maturation during engulfment of apoptotic cells."
      Almendinger J., Doukoumetzidis K., Kinchen J.M., Kaech A., Ravichandran K.S., Hengartner M.O.
      PLoS ONE 6:E18325-E18325(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DOMAIN, DISRUPTION PHENOTYPE, MUTAGENESIS OF 265-ARG--LYS-267.
    6. "Two PI 3-kinases and one PI 3-phosphatase together establish the cyclic waves of phagosomal PtdIns(3)P critical for the degradation of apoptotic cells."
      Lu N., Shen Q., Mahoney T.R., Neukomm L.J., Wang Y., Zhou Z.
      PLoS Biol. 10:E1001245-E1001245(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.

    Entry informationi

    Entry nameiLST4_CAEEL
    AccessioniPrimary (citable) accession number: Q8I4E2
    Secondary accession number(s): D3NQ98
    , J7SA60, Q8I4E1, Q9XXG2, Q9XXG3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 26, 2013
    Last sequence update: March 1, 2003
    Last modified: October 1, 2014
    This is version 90 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programCaenorhabditis annotation project

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Caenorhabditis elegans
      Caenorhabditis elegans: entries, gene names and cross-references to WormBase
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3