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Protein

Lissencephaly-1 homolog B

Gene

pafah1b1b

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus end. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the peripheral transport of microtubule fragments and the coupling of the nucleus and centrosome. May be required for proliferation of neuronal precursors and neuronal migration (By similarity). Involved in the positioning of nuclei in photoreceptor cells.UniRule annotation1 Publication

GO - Biological processi

  • apical protein localization Source: ZFIN
  • brain morphogenesis Source: ZFIN
  • cell differentiation Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • establishment of mitotic spindle orientation Source: UniProtKB-HAMAP
  • establishment of nucleus localization Source: ZFIN
  • mitotic nuclear division Source: UniProtKB-KW
  • photoreceptor cell maintenance Source: ZFIN
  • transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Cell cycle, Cell division, Differentiation, Mitosis, Neurogenesis, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
Lissencephaly-1 homolog BUniRule annotation
Alternative name(s):
Platelet-activating factor acetylhydrolase IB subunit alpha bUniRule annotation
Gene namesi
Name:pafah1b1b
Synonyms:lis1aUniRule annotation
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Unplaced

Organism-specific databases

ZFINiZDB-GENE-040116-3. pafah1b1b.

Subcellular locationi

  • Cytoplasmcytoskeleton UniRule annotation
  • Cytoplasmcytoskeletonmicrotubule organizing centercentrosome UniRule annotation

  • Note: Localizes to the plus end of microtubules and to the centrosome.UniRule annotation

GO - Cellular componenti

  • cytoplasm Source: ZFIN
  • microtubule Source: UniProtKB-KW
  • microtubule associated complex Source: UniProtKB-HAMAP
  • microtubule organizing center Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Microtubule

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedUniRule annotation
Chaini2 – 410409Lissencephaly-1 homolog BPRO_0000240417Add
BLAST

Proteomic databases

PaxDbiQ803D2.
PRIDEiQ803D2.

Expressioni

Tissue specificityi

Enriched in the photoreceptor cell layer.1 Publication

Gene expression databases

BgeeiQ803D2.

Interactioni

Subunit structurei

Can self-associate. Interacts with dynein, dynactin, nde1 and ndel1.UniRule annotation

Protein-protein interaction databases

STRINGi7955.ENSDARP00000039257.

Structurei

3D structure databases

ProteinModelPortaliQ803D2.
SMRiQ803D2. Positions 1-78, 92-408.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 3933LisHUniRule annotationAdd
BLAST
Repeati106 – 14742WD 1Add
BLAST
Repeati148 – 18740WD 2Add
BLAST
Repeati190 – 22940WD 3Add
BLAST
Repeati232 – 27140WD 4Add
BLAST
Repeati274 – 33360WD 5Add
BLAST
Repeati336 – 37742WD 6Add
BLAST
Repeati379 – 41032WD 7Add
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili56 – 8227UniRule annotationAdd
BLAST

Domaini

Dimerization mediated by the LisH domain may be required to activate dynein.UniRule annotation

Sequence similaritiesi

Belongs to the WD repeat LIS1/nudF family.UniRule annotation
Contains 1 LisH domain.UniRule annotation
Contains 7 WD repeats.UniRule annotation

Keywords - Domaini

Coiled coil, Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0295. Eukaryota.
ENOG410XP3K. LUCA.
HOGENOMiHOG000184015.
HOVERGENiHBG006271.
InParanoidiQ803D2.
KOiK16794.
OrthoDBiEOG7QZG9N.
PhylomeDBiQ803D2.
TreeFamiTF105741.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
HAMAPiMF_03141. lis1.
InterProiIPR017252. Dynein_regulator_LIS1.
IPR020472. G-protein_beta_WD-40_rep.
IPR006594. LisH.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF08513. LisH. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]
PIRSFiPIRSF037647. Dynein_regulator_Lis1. 1 hit.
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00667. LisH. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50896. LISH. 1 hit.
PS00678. WD_REPEATS_1. 4 hits.
PS50082. WD_REPEATS_2. 7 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q803D2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVLSQRQRDE LNRAIADYLR SNGYEEAYST FKKEAELDVN DELDKKFAGL
60 70 80 90 100
LEKKWTSVIR LQKKVMELES KLNEAKEEIT LGGPVGQKRD PKEWIPRPPE
110 120 130 140 150
KYALSGHRSP VTRVIFHPVF SLMVSASEDA TIKVWDYEAG DFERTLKGHT
160 170 180 190 200
DSVQDISFDQ TGKLLASCSA DMTIKLWDFQ GFECIRTMHG HDHNVSSVAI
210 220 230 240 250
MPNGDHIVSA SRDKTMKMWE VATGYCVKTF TGHREWVRMV RPNQDGTLLA
260 270 280 290 300
SCSNDQTVRV WVVATKECKA ELREHEHVVE CISWAPESAH PTISEATGSE
310 320 330 340 350
NKKSGKPGPF LLSGSRDKTI KMWDISTGMC LMTLVGHDNW VRGVLFHPGG
360 370 380 390 400
RFVVSCADDK TLRIWDYKNK RCMKTLSAHE HFVTSLDFHK ASPYVVTGSV
410
DQTVKVWECR
Length:410
Mass (Da):46,530
Last modified:January 23, 2007 - v3
Checksum:i23FC732F50D0E562
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti391 – 3911A → T in ABA29741 (PubMed:17785424).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ141216 mRNA. Translation: ABA29741.1.
BC044530 mRNA. Translation: AAH44530.1.
RefSeqiNP_958503.1. NM_201346.1.
UniGeneiDr.79815.

Genome annotation databases

GeneIDi394247.
KEGGidre:394247.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ141216 mRNA. Translation: ABA29741.1.
BC044530 mRNA. Translation: AAH44530.1.
RefSeqiNP_958503.1. NM_201346.1.
UniGeneiDr.79815.

3D structure databases

ProteinModelPortaliQ803D2.
SMRiQ803D2. Positions 1-78, 92-408.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000039257.

Proteomic databases

PaxDbiQ803D2.
PRIDEiQ803D2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi394247.
KEGGidre:394247.

Organism-specific databases

CTDi394247.
ZFINiZDB-GENE-040116-3. pafah1b1b.

Phylogenomic databases

eggNOGiKOG0295. Eukaryota.
ENOG410XP3K. LUCA.
HOGENOMiHOG000184015.
HOVERGENiHBG006271.
InParanoidiQ803D2.
KOiK16794.
OrthoDBiEOG7QZG9N.
PhylomeDBiQ803D2.
TreeFamiTF105741.

Miscellaneous databases

NextBioi20815156.
PROiQ803D2.

Gene expression databases

BgeeiQ803D2.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
HAMAPiMF_03141. lis1.
InterProiIPR017252. Dynein_regulator_LIS1.
IPR020472. G-protein_beta_WD-40_rep.
IPR006594. LisH.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF08513. LisH. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]
PIRSFiPIRSF037647. Dynein_regulator_Lis1. 1 hit.
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00667. LisH. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS50896. LISH. 1 hit.
PS00678. WD_REPEATS_1. 4 hits.
PS50082. WD_REPEATS_2. 7 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Mechanism of positioning the cell nucleus in vertebrate photoreceptors."
    Tsujikawa M., Omori Y., Biyanwila J., Malicki J.
    Proc. Natl. Acad. Sci. U.S.A. 104:14819-14824(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: AB.

Entry informationi

Entry nameiLIS1B_DANRE
AccessioniPrimary (citable) accession number: Q803D2
Secondary accession number(s): Q07DR2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 115 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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 one 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.