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Q8I4E2

- LST4_CAEEL

UniProt

Q8I4E2 - LST4_CAEEL

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Protein

Sorting nexin lst-4

Gene

lst-4

Organism
Caenorhabditis elegans
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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 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
Complete GO annotation...

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. membrane Source: UniProtKB-KW
  3. phagocytic vesicle Source: WormBase
Complete GO annotation...

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. 1 Publication
Mutagenesisi265 – 2651R → Q: Defect recruitment by phosphoinositide to phagosomal surface. 1 Publication
Mutagenesisi494 – 4941K → E: Defective recruitment to the phagosome. 1 Publication
Mutagenesisi501 – 5011R → E: Defective recruitment to the phagosome. 1 Publication

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

Gene expression databases

ExpressionAtlasiQ8I4E2. baseline.

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

        10         20         30         40         50
MAQVKAEYDF QSQPNTGELS ISAGEVLTVI RENIDGGWIE GRNVRGSVGL
60 70 80 90 100
FPESYVTPYQ ASRPPPVLPP PLPPTSSGPP AASSRPFDDW GGASEVAAPP
110 120 130 140 150
SYGAQHHHQP TPSVPEVTRS SYPSQNDDFD DEWTDEDDEQ EPTRPNVQSS
160 170 180 190 200
IGSNSRRDLS RSHSEHGGPD RGSNKVNKNI NRFSNFVKSG VEAYVIGESK
210 220 230 240 250
TTSQISERHE VVMNNGIIQW KPIQQYYTCI VDKPKKESKL KGLKSFIAYS
260 270 280 290 300
ITSSLTNIQR QVSRRYKHFD WLHEQLSAKY VLIPIPPLPE KQVAGRYEED
310 320 330 340 350
LIDHRKHILQ LWVNKICRHP VLSQSEVWLH FISCTDEKDW KNGKRRAEKD
360 370 380 390 400
EYIGGAFLNC ITVPHQPLDP NNVDMQVERF QRSVKTSEEA MRVMQERMNM
410 420 430 440 450
FQKVFAGPVK QNWQKMGSAF KTLQQSFEID ETVASRRLTE ALAYTASEYH
460 470 480 490 500
EIGQVFDAHT KNDMEPVLEN LYSYKGTVQN VPDIIQVHKQ AVQKFRDSEG
510 520 530 540 550
RLSSAEAEKM KQRIDAMSYT VIAEVQHQTA EKVEDMKSTM GTYLKKQAMF
560
YQEVATKLTS LAARYD

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.

Gene expression databases

ExpressionAtlasi Q8I4E2. baseline.

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

« Hide 'large scale' publications
  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 29, 2014
This is version 91 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