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Protein

Nuclear distribution protein nudE-like 1

Gene

Ndel1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for organization of the cellular microtubule array and microtubule anchoring at the centrosome. May regulate microtubule organization at least in part by targeting the microtubule severing protein KATNA1 to the centrosome. Also 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 ends. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the centripetal motion of secretory vesicles and the coupling of the nucleus and centrosome. Also required during brain development for the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Required for mitosis in some cell types but appears to be dispensible for mitosis in cortical neuronal progenitors, which instead requires NDE1. Facilitates the polymerization of neurofilaments from the individual subunits NEFH and NEFL (By similarity). Plays a role, together with DISC1, in the regulation of neurite outgrowth.By similarity1 Publication

GO - Molecular functioni

  • oligopeptidase activity Source: RGD
  • protein complex binding Source: RGD

GO - Biological processi

  • activation of GTPase activity Source: Ensembl
  • central nervous system neuron axonogenesis Source: Ensembl
  • centrosome localization Source: Ensembl
  • cerebral cortex radially oriented cell migration Source: Ensembl
  • chromosome segregation Source: Ensembl
  • inner cell mass cell proliferation Source: Ensembl
  • mitotic centrosome separation Source: Ensembl
  • neurofilament cytoskeleton organization Source: Ensembl
  • neuron migration Source: Ensembl
  • neuron projection development Source: RGD
  • neuron projection extension Source: Ensembl
  • nuclear envelope disassembly Source: MGI
  • positive regulation of axon extension Source: RGD
  • positive regulation of axon regeneration Source: RGD
  • proteolysis Source: GOC
  • regulation of intracellular protein transport Source: Ensembl
  • regulation of neuron projection development Source: UniProtKB
  • retrograde axonal transport Source: Ensembl
  • vesicle transport along microtubule Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis, Transport

Enzyme and pathway databases

ReactomeiR-RNO-2467813. Separation of Sister Chromatids.
R-RNO-2500257. Resolution of Sister Chromatid Cohesion.
R-RNO-5663220. RHO GTPases Activate Formins.
R-RNO-68877. Mitotic Prometaphase.

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear distribution protein nudE-like 1
Short name:
Protein Nudel
Gene namesi
Name:Ndel1
Synonyms:Nude2, Nudel
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 10

Organism-specific databases

RGDi621235. Ndel1.

Subcellular locationi

GO - Cellular componenti

  • axon Source: RGD
  • axon cytoplasm Source: GOC
  • axon hillock Source: Ensembl
  • cell body Source: RGD
  • cell leading edge Source: Ensembl
  • centrosome Source: UniProtKB
  • condensed chromosome kinetochore Source: UniProtKB-SubCell
  • cytoplasm Source: RGD
  • kinesin complex Source: RGD
  • microtubule Source: UniProtKB-KW
  • neurofilament cytoskeleton Source: Ensembl
  • nuclear envelope Source: MGI
  • spindle Source: UniProtKB-SubCell
  • synaptic vesicle Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Cytoplasm, Cytoskeleton, Kinetochore, Microtubule

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 345345Nuclear distribution protein nudE-like 1PRO_0000240215Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei215 – 2151PhosphoserineBy similarity
Modified residuei219 – 2191Phosphothreonine; by CDK1 and MAPK1By similarity
Modified residuei242 – 2421Phosphoserine; by CDK1By similarity
Modified residuei245 – 2451Phosphothreonine; by CDK1 and MAPK1By similarity
Lipidationi273 – 2731S-palmitoyl cysteine; by ZDHHC2, ZDHHC3 and ZDHHC7By similarity
Modified residuei344 – 3441PhosphoserineCombined sources

Post-translational modificationi

Phosphorylated in mitosis. Can be phosphorylated by CDK1, CDK5 and MAPK1. Phosphorylation by CDK5 promotes interaction with KATNA1 and YWHAE (By similarity).By similarity
Palmitoylation at Cys-273 reduces affinity for dynein.By similarity

Keywords - PTMi

Lipoprotein, Palmitate, Phosphoprotein

Proteomic databases

PaxDbiQ78PB6.
PRIDEiQ78PB6.

PTM databases

iPTMnetiQ78PB6.
PhosphoSiteiQ78PB6.

Expressioni

Inductioni

Up-regulated during neurite outgrowth upon differentiation with NGF.1 Publication

Gene expression databases

GenevisibleiQ78PB6. RN.

Interactioni

Subunit structurei

Self-associates. Interacts with dynactin, tubulin gamma, KATNA1, KATNB1, microtubules, PCM1, PCNT, and YWHAE. Interacts directly with NEFL and indirectly with NEFH. Interacts (via C-terminus) with CENPF (By similarity). Interacts with DISC1, dynein and PAFAH1B1. Interacts with ZNF365 (By similarity).By similarity

GO - Molecular functioni

  • protein complex binding Source: RGD

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000005574.

Structurei

Secondary structure

1
345
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 164153Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V71X-ray2.24A/B8-193[»]
ProteinModelPortaliQ78PB6.
SMRiQ78PB6. Positions 8-168.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ78PB6.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni56 – 166111Self-associationBy similarityAdd
BLAST
Regioni64 – 189126Interaction with KATNB1By similarityAdd
BLAST
Regioni114 – 13320Required for interaction with PAFAH1B1By similarityAdd
BLAST
Regioni175 – 345171Interaction with CENPFBy similarityAdd
BLAST
Regioni189 – 25668Interaction with YWHAEBy similarityAdd
BLAST
Regioni191 – 345155Interaction with NEFLBy similarityAdd
BLAST
Regioni195 – 25662Interaction with KATNA1By similarityAdd
BLAST
Regioni227 – 27852Interaction with DISC1By similarityAdd
BLAST
Regioni256 – 29136Required for localization to the centrosome and interaction with dynein, dynactin, tubulin gamma, PCM1 and PCNTBy similarityAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili28 – 190163Sequence analysisAdd
BLAST

Sequence similaritiesi

Belongs to the nudE family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG1853. Eukaryota.
ENOG410XPMP. LUCA.
GeneTreeiENSGT00390000000111.
HOGENOMiHOG000280681.
HOVERGENiHBG082010.
InParanoidiQ78PB6.
KOiK16739.
OMAiQAFLIMD.
OrthoDBiEOG74R1R5.
PhylomeDBiQ78PB6.
TreeFamiTF325693.

Family and domain databases

InterProiIPR006964. NUDE_dom.
[Graphical view]
PfamiPF04880. NUDE_C. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q78PB6-1) [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
MDGEDIPDFS SLKEETAYWK ELSLKYKQSF QEARDELVEF QEGSRELEAE
60 70 80 90 100
LEAQLVQAEQ RNRDLQADNQ RLKYEVEALK EKLEHQYAQS YKQVSVLEDD
110 120 130 140 150
LSQTRAIKEQ LHKYVRELEQ ANDDLERAKR ATIVSLEDFE QRLNQAIERN
160 170 180 190 200
AFLESELDEK ESLLVSVQRL KDEARDLRQE LAVRERQQEV TRKSAPSSPT
210 220 230 240 250
LDCEKMDSAV QASLSLPATP VGKGTENSFP SPKAIPNGFG TSPLTPSARI
260 270 280 290 300
SALNIVGDLL RKVGALESKL AACRNFAKDQ ASRKSYVPGS VNCGVMNSNG
310 320 330 340
PECPRSGRAT FFHKGAVNGF DPAPPPPGLG SSRPSSAPGM LPLSV
Length:345
Mass (Da):38,366
Last modified:July 5, 2004 - v1
Checksum:iCB3059DFD998E9EC
GO
Isoform 2 (identifier: Q78PB6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     316-328: AVNGFDPAPPPPG → QEKVIFPTLFMGQ
     329-345: Missing.

Note: No experimental confirmation available.
Show »
Length:328
Mass (Da):37,030
Checksum:iEDB7973DEE2DA190
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti42 – 421E → Q in AAH70909 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei316 – 32813AVNGF…PPPPG → QEKVIFPTLFMGQ in isoform 2. 1 PublicationVSP_019312Add
BLAST
Alternative sequencei329 – 34517Missing in isoform 2. 1 PublicationVSP_019313Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY008298 mRNA. Translation: AAG21830.1.
BC070909 mRNA. Translation: AAH70909.1.
RefSeqiNP_579854.1. NM_133320.1. [Q78PB6-1]
XP_006246640.1. XM_006246578.2. [Q78PB6-2]
UniGeneiRn.2947.

Genome annotation databases

EnsembliENSRNOT00000005574; ENSRNOP00000005574; ENSRNOG00000004139. [Q78PB6-1]
ENSRNOT00000065505; ENSRNOP00000062145; ENSRNOG00000004139. [Q78PB6-2]
GeneIDi170845.
KEGGirno:170845.
UCSCiRGD:621235. rat. [Q78PB6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY008298 mRNA. Translation: AAG21830.1.
BC070909 mRNA. Translation: AAH70909.1.
RefSeqiNP_579854.1. NM_133320.1. [Q78PB6-1]
XP_006246640.1. XM_006246578.2. [Q78PB6-2]
UniGeneiRn.2947.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V71X-ray2.24A/B8-193[»]
ProteinModelPortaliQ78PB6.
SMRiQ78PB6. Positions 8-168.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000005574.

PTM databases

iPTMnetiQ78PB6.
PhosphoSiteiQ78PB6.

Proteomic databases

PaxDbiQ78PB6.
PRIDEiQ78PB6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000005574; ENSRNOP00000005574; ENSRNOG00000004139. [Q78PB6-1]
ENSRNOT00000065505; ENSRNOP00000062145; ENSRNOG00000004139. [Q78PB6-2]
GeneIDi170845.
KEGGirno:170845.
UCSCiRGD:621235. rat. [Q78PB6-1]

Organism-specific databases

CTDi81565.
RGDi621235. Ndel1.

Phylogenomic databases

eggNOGiKOG1853. Eukaryota.
ENOG410XPMP. LUCA.
GeneTreeiENSGT00390000000111.
HOGENOMiHOG000280681.
HOVERGENiHBG082010.
InParanoidiQ78PB6.
KOiK16739.
OMAiQAFLIMD.
OrthoDBiEOG74R1R5.
PhylomeDBiQ78PB6.
TreeFamiTF325693.

Enzyme and pathway databases

ReactomeiR-RNO-2467813. Separation of Sister Chromatids.
R-RNO-2500257. Resolution of Sister Chromatid Cohesion.
R-RNO-5663220. RHO GTPases Activate Formins.
R-RNO-68877. Mitotic Prometaphase.

Miscellaneous databases

EvolutionaryTraceiQ78PB6.
PROiQ78PB6.

Gene expression databases

GenevisibleiQ78PB6. RN.

Family and domain databases

InterProiIPR006964. NUDE_dom.
[Graphical view]
PfamiPF04880. NUDE_C. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Functional analysis of NUDE that interacts with LIS1, the lissencephaly gene product."
    Umezu M., Kitagawa M., Aoki J., Arai H.
    Submitted (SEP-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: Sprague-Dawley.
    Tissue: Liver.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Heart.
  3. "NUDEL is a novel cdk5 substrate that associates with LIS1 and cytoplasmic dynein."
    Niethammer M., Smith D.S., Ayala R., Peng J., Ko J., Lee M.-S., Morabito M., Tsai L.-H.
    Neuron 28:697-711(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PAFAH1B1 AND DYNEIN, SUBCELLULAR LOCATION.
    Tissue: Brain.
  4. Cited for: PUTATIVE FUNCTION AS AN OLIGOPEPTIDASE.
  5. "DISC1-NDEL1/NUDEL protein interaction, an essential component for neurite outgrowth, is modulated by genetic variations of DISC1."
    Kamiya A., Tomoda T., Chang J., Takaki M., Zhan C., Morita M., Cascio M.B., Elashvili S., Koizumi H., Takanezawa Y., Dickerson F., Yolken R., Arai H., Sawa A.
    Hum. Mol. Genet. 15:3313-3323(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH DISC1, INDUCTION, SUBCELLULAR LOCATION.
  6. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-344, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNDEL1_RAT
AccessioniPrimary (citable) accession number: Q78PB6
Secondary accession number(s): Q6IRI4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 13, 2006
Last sequence update: July 5, 2004
Last modified: June 8, 2016
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

Was originally thought to function as an oligopeptidase (NUDEL-oligopeptidase or endooligopeptidase A) which could regulate peptide levels relevant to brain function.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.