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Q8I4E2 (LST4_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 88. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Sorting nexin lst-4
Alternative name(s):
Lateral signaling target protein 4
Gene names
Name:lst-4
ORF Names:Y37A1B.2
OrganismCaenorhabditis elegans [Reference proteome]
Taxonomic identifier6239 [NCBI]
Taxonomic lineageEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis

Protein attributes

Sequence length566 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.3 Ref.4 Ref.5

Subunit structure

Homodimer. Isoform d interacts (via SH3 domain) with dyn-1. Ref.4

Subcellular location

Cytoplasm. Cytoplasmic vesiclephagosome membrane. Note: Recruited to phagosomal surface by phosphatidylinositol trisphosphate. BAR and PX domains are required for the phagosomal localization. Ref.1 Ref.4 Ref.5 Ref.6

Tissue specificity

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

Developmental stage

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. Ref.2

Domain

The BAR and PX domains are required for recruitment to the phagosome. Ref.4 Ref.5

The SH3 domain is involved in phagosome maturation. Ref.4 Ref.5

Disruption phenotype

Aberrant vulval development, ectopic vulval induction, retained cell corpses and defective recruitment of dyn-1 and rab-7 to phagosomal surfaces. Ref.2 Ref.4 Ref.5

Sequence similarities

Belongs to the sorting nexin family.

Contains 1 BAR domain.

Contains 1 PX (phox homology) domain.

Contains 1 SH3 domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

dyn-1P390554EBI-4325777,EBI-317945

Alternative products

This entry describes 6 isoforms produced by alternative splicing. [Align] [Select]
Isoform c Ref.1 (identifier: Q8I4E2-1)

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.
Note: No experimental confirmation available.
Isoform a Ref.1 (identifier: Q8I4E2-2)

The sequence of this isoform differs from the canonical sequence as follows:
     141-163: EPTRPNVQSSIGSNSRRDLSRSH → VFLKFYFNFLIVQFLSVLFIPSN
     165-566: Missing.
Note: No experimental confirmation available.
Isoform b Ref.1 (identifier: Q8I4E2-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-66: MAQVKAEYDF...TPYQASRPPP → MLFTSSLRKA...FKKSGAISKS
Note: No experimental confirmation available.
Isoform d Ref.1 (identifier: Q8I4E2-4)

The sequence of this isoform differs from the canonical sequence as follows:
     260-261: Missing.
Note: No experimental confirmation available.
Isoform e Ref.1 (identifier: Q8I4E2-5)

The sequence of this isoform differs from the canonical sequence as follows:
     1-509: Missing.
Note: No experimental confirmation available.
Isoform f Ref.1 (identifier: Q8I4E2-6)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 566566Sorting nexin lst-4
PRO_0000422772

Regions

Domain1 – 6161SH3
Domain227 – 339113PX
Domain362 – 566205BAR
Compositional bias64 – 11552Pro-rich

Natural variations

Alternative sequence1 – 509509Missing in isoform e. Ref.1
VSP_046628
Alternative sequence1 – 6666MAQVK…SRPPP → MLFTSSLRKAVENYPTPPGG SSEDAHRQLLERRRKQMLRR HTCSTLIKQDTSASPHKMKP PILMEEEDEQHSTGKHSSRK SSFKKSGAISKS in isoform b. Ref.1
VSP_046629
Alternative sequence2 – 7978AQVKA…TSSGP → STDDETRSSQQDGAYPSSKR NGSVGSSTRSTSTKKRLSRQ DSTARRRRLSEERDSRRRVE KSVSSCLSSNRSHHDQNK in isoform f. Ref.1
VSP_046630
Alternative sequence80 – 14061Missing in isoform f. Ref.1
VSP_046631
Alternative sequence141 – 16323EPTRP…LSRSH → VFLKFYFNFLIVQFLSVLFI PSN in isoform a. Ref.1
VSP_046632
Alternative sequence165 – 566402Missing in isoform a. Ref.1
VSP_046633
Alternative sequence260 – 2612Missing in isoform d. Ref.1
VSP_046634

Experimental info

Mutagenesis265 – 2673RYK → QAA: Defective recruitment to the phagosome. Ref.4 Ref.5
Mutagenesis2651R → Q: Defect recruitment by phosphoinositide to phagosomal surface. Ref.4
Mutagenesis4941K → E: Defective recruitment to the phagosome. Ref.4
Mutagenesis5011R → E: Defective recruitment to the phagosome. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform c [UniParc].

Last modified March 1, 2003. Version 1.
Checksum: 77CFBE901A3E3B24

FASTA56664,329
        10         20         30         40         50         60 
MAQVKAEYDF QSQPNTGELS ISAGEVLTVI RENIDGGWIE GRNVRGSVGL FPESYVTPYQ 

        70         80         90        100        110        120 
ASRPPPVLPP PLPPTSSGPP AASSRPFDDW GGASEVAAPP SYGAQHHHQP TPSVPEVTRS 

       130        140        150        160        170        180 
SYPSQNDDFD DEWTDEDDEQ EPTRPNVQSS IGSNSRRDLS RSHSEHGGPD RGSNKVNKNI 

       190        200        210        220        230        240 
NRFSNFVKSG VEAYVIGESK TTSQISERHE VVMNNGIIQW KPIQQYYTCI VDKPKKESKL 

       250        260        270        280        290        300 
KGLKSFIAYS ITSSLTNIQR QVSRRYKHFD WLHEQLSAKY VLIPIPPLPE KQVAGRYEED 

       310        320        330        340        350        360 
LIDHRKHILQ LWVNKICRHP VLSQSEVWLH FISCTDEKDW KNGKRRAEKD EYIGGAFLNC 

       370        380        390        400        410        420 
ITVPHQPLDP NNVDMQVERF QRSVKTSEEA MRVMQERMNM FQKVFAGPVK QNWQKMGSAF 

       430        440        450        460        470        480 
KTLQQSFEID ETVASRRLTE ALAYTASEYH EIGQVFDAHT KNDMEPVLEN LYSYKGTVQN 

       490        500        510        520        530        540 
VPDIIQVHKQ AVQKFRDSEG RLSSAEAEKM KQRIDAMSYT VIAEVQHQTA EKVEDMKSTM 

       550        560 
GTYLKKQAMF YQEVATKLTS LAARYD 

« Hide

Isoform a [UniParc].

Checksum: 090A42146AAC080C
Show »

FASTA16418,014
Isoform b [UniParc].

Checksum: 156B568888CD5E78
Show »

FASTA59267,553
Isoform d [UniParc].

Checksum: 224A0F3052A1CA3D
Show »

FASTA56464,045
Isoform e [UniParc].

Checksum: 5AE1F0267B8630F8
Show »

FASTA576,580
Isoform f [UniParc].

Checksum: 1514E1BFE36F43FE
Show »

FASTA50558,155

References

« Hide 'large scale' references
[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 N2.
[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]"A pathway for phagosome maturation during engulfment of apoptotic cells."
Kinchen J.M., Doukoumetzidis K., Almendinger J., Stergiou L., Tosello-Trampont A., Sifri C.D., Hengartner M.O., Ravichandran K.S.
Nat. Cell Biol. 10:556-566(2008) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_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]
UniGeneCel.22885.

3D structure databases

ProteinModelPortalQ8I4E2.
SMRQ8I4E2. Positions 7-56, 190-566.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ8I4E2. 6 interactions.
STRING6239.Y37A1B.2b.

Proteomic databases

PRIDEQ8I4E2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaY37A1B.2c; Y37A1B.2c; WBGene00003086. [Q8I4E2-1]
GeneID178361.
KEGGcel:CELE_Y37A1B.2.
UCSCY37A1B.2b. c. elegans. [Q8I4E2-1]

Organism-specific databases

CTD178361.
WormBaseY37A1B.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

GeneTreeENSGT00510000046469.
HOGENOMHOG000261633.
KOK17923.
OMASAIYLEI.

Family and domain databases

Gene3D3.30.1520.10. 1 hit.
InterProIPR028650. Lst-4.
IPR001683. Phox.
IPR001452. SH3_domain.
IPR014536. Snx9_subfam.
IPR019497. Sorting_nexin_WASP-bd-dom.
[Graphical view]
PANTHERPTHR10555:SF11. PTHR10555:SF11. 1 hit.
PfamPF10456. BAR_3_WASP_bdg. 1 hit.
PF00787. PX. 1 hit.
PF14604. SH3_9. 1 hit.
[Graphical view]
PIRSFPIRSF027744. Snx9. 1 hit.
PRINTSPR00452. SH3DOMAIN.
SMARTSM00312. PX. 1 hit.
SM00326. SH3. 1 hit.
[Graphical view]
SUPFAMSSF50044. SSF50044. 1 hit.
SSF64268. SSF64268. 1 hit.
PROSITEPS50195. PX. 1 hit.
PS50002. SH3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio900810.

Entry information

Entry nameLST4_CAEEL
AccessionPrimary (citable) accession number: Q8I4E2
Secondary accession number(s): D3NQ98 expand/collapse secondary AC list , J7SA60, Q8I4E1, Q9XXG2, Q9XXG3
Entry history
Integrated into UniProtKB/Swiss-Prot: June 26, 2013
Last sequence update: March 1, 2003
Last modified: July 9, 2014
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Relevant documents

SIMILARITY comments

Index of protein domains and families

Caenorhabditis elegans

Caenorhabditis elegans: entries, gene names and cross-references to WormBase