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Protein

Neuroplastin

Gene

Nptn

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

Functioni

Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity.

GO - Molecular functioni

  • cell adhesion molecule binding Source: HGNC
  • fibroblast growth factor receptor binding Source: RGD
  • ion channel binding Source: RGD
  • transmembrane receptor protein tyrosine kinase activity Source: InterPro
  • type 1 fibroblast growth factor receptor binding Source: UniProtKB

GO - Biological processi

  • homophilic cell adhesion via plasma membrane adhesion molecules Source: HGNC
  • long-term synaptic potentiation Source: UniProtKB
  • positive regulation of cellular protein localization Source: RGD
  • positive regulation of cytosolic calcium ion concentration Source: UniProtKB
  • positive regulation of ERK1 and ERK2 cascade Source: RGD
  • positive regulation of fibroblast growth factor receptor signaling pathway Source: UniProtKB
  • positive regulation of long-term neuronal synaptic plasticity Source: HGNC
  • positive regulation of long-term synaptic potentiation Source: RGD
  • positive regulation of neuron projection development Source: UniProtKB
  • positive regulation of protein phosphorylation Source: UniProtKB
  • regulation of cell adhesion Source: HGNC
  • synaptic transmission Source: Reactome
  • transmembrane receptor protein tyrosine kinase signaling pathway Source: InterPro
  • visual learning Source: RGD
Complete GO annotation...

Keywords - Biological processi

Cell adhesion, Neurogenesis

Enzyme and pathway databases

ReactomeiR-RNO-112314. Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell.

Names & Taxonomyi

Protein namesi
Recommended name:
Neuroplastin
Alternative name(s):
Glycoprotein 55/65
Short name:
gp55/65
Stromal cell-derived receptor 1
Short name:
SDR-1
Gene namesi
Name:Nptn
Synonyms:Sdfr1, Sdr1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 8

Organism-specific databases

RGDi620296. Nptn.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini29 – 338310ExtracellularSequence analysisAdd
BLAST
Transmembranei339 – 35921HelicalSequence analysisAdd
BLAST
Topological domaini360 – 39334CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • cell Source: GOC
  • cell surface Source: RGD
  • dendrite Source: RGD
  • inhibitory synapse Source: RGD
  • integral component of membrane Source: BHF-UCL
  • plasma membrane Source: Reactome
  • postsynaptic density Source: RGD
  • postsynaptic membrane Source: HGNC
  • presynaptic membrane Source: HGNC
  • synaptic membrane Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2828By similarityAdd
BLAST
Chaini29 – 393365NeuroplastinPRO_0000394472Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi52 ↔ 116PROSITE-ProRule annotation
Disulfide bondi169 ↔ 217PROSITE-ProRule annotation1 Publication
Glycosylationi170 – 1701N-linked (GlcNAc...)1 Publication
Glycosylationi196 – 1961N-linked (GlcNAc...)Sequence analysis
Glycosylationi228 – 2281N-linked (GlcNAc...)1 Publication
Disulfide bondi258 ↔ 315PROSITE-ProRule annotation1 Publication
Glycosylationi283 – 2831N-linked (GlcNAc...)1 Publication
Glycosylationi295 – 2951N-linked (GlcNAc...)1 Publication
Glycosylationi316 – 3161N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

Isoform 1 and isoform 2 are N-glycosylated.2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiP97546.
PRIDEiP97546.

PTM databases

iPTMnetiP97546.
PhosphoSiteiP97546.
SwissPalmiP97546.
UniCarbKBiP97546.

Expressioni

Tissue specificityi

Isoform 1 is ubiquitously expressed. Isoform 2 is brain-specific. In brain isoform 2 is highly expressed in hippocampus and cerebral cortex and weakly in cerebellum and lower brain regions. In the hippocampus isoform 2 is found in the dentate gyrus and CA1-CA4, the striatum oriens of CA3 shows the higher level.2 Publications

Developmental stagei

Isoform 1 is detectable at all developmental stages starting from postnatal day 1. Isoform 2 is low at postnatal day 1, increases steadily until postnatal days 20-25 and then declines to an intermediate level.1 Publication

Gene expression databases

ExpressionAtlasiP97546. baseline and differential.
GenevisibleiP97546. RN.

Interactioni

GO - Molecular functioni

  • cell adhesion molecule binding Source: HGNC
  • fibroblast growth factor receptor binding Source: RGD
  • ion channel binding Source: RGD
  • type 1 fibroblast growth factor receptor binding Source: UniProtKB

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000012091.

Structurei

Secondary structure

1
393
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi149 – 1524Combined sources
Beta strandi161 – 1633Combined sources
Beta strandi165 – 1739Combined sources
Beta strandi178 – 1858Combined sources
Beta strandi198 – 2069Combined sources
Helixi209 – 2113Combined sources
Beta strandi213 – 2219Combined sources
Beta strandi224 – 23411Combined sources
Beta strandi238 – 2425Combined sources
Beta strandi244 – 2496Combined sources
Beta strandi254 – 2618Combined sources
Beta strandi267 – 2748Combined sources
Beta strandi277 – 2804Combined sources
Beta strandi288 – 2925Combined sources
Beta strandi294 – 3018Combined sources
Turni306 – 3083Combined sources
Beta strandi311 – 3188Combined sources
Beta strandi323 – 33311Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WV3X-ray1.95A148-333[»]
ProteinModelPortaliP97546.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP97546.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini29 – 134106Ig-like 1Add
BLAST
Domaini148 – 23487Ig-like 2Add
BLAST
Domaini237 – 32791Ig-like 3Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni149 – 16113Narpin; mediates binding with FGFR1 and has antidepressant-like activityAdd
BLAST

Domaini

Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1.

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IJET. Eukaryota.
ENOG4111V1Q. LUCA.
GeneTreeiENSGT00390000010516.
HOGENOMiHOG000263411.
HOVERGENiHBG008120.
InParanoidiP97546.
PhylomeDBiP97546.

Family and domain databases

Gene3Di2.60.40.10. 3 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR027112. Neuroplastin.
IPR016243. Tyr_kinase_CSF1/PDGF_rcpt.
[Graphical view]
PANTHERiPTHR10075:SF5. PTHR10075:SF5. 1 hit.
PIRSFiPIRSF000615. TyrPK_CSF1-R. 1 hit.
SMARTiSM00409. IG. 3 hits.
SM00408. IGc2. 2 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 3 hits.
PROSITEiPS50835. IG_LIKE. 3 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 2 (identifier: P97546-2) [UniParc]FASTAAdd to basket

Also known as: gp65, np65

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
MSGSSLPGAL ALSLLLVSGS LLPGPGAAQN AGFVKSPMSE TKLTGDAFEL
60 70 80 90 100
YCDVVGSPTP EIQWWYAEVN RAESFRQLWD GARKRRVTVN TAYGSNGVSV
110 120 130 140 150
LRITRLTLED SGTYECRASN DPKRNDLRQN PSITWIRAQA TISVLQKPRI
160 170 180 190 200
VTSEEVIIRD SLLPVTLQCN LTSSSHTLMY SYWTKNGVEL TATRKNASNM
210 220 230 240 250
EYRINKPRAE DSGEYHCVYH FVSAPKANAT IEVKAAPDIT GHKRSENKNE
260 270 280 290 300
GQDAMMYCKS VGYPHPEWMW RKKENGVFEE ISNSSGRFFI INKENYTELN
310 320 330 340 350
IVNLQITEDP GEYECNATNS IGSASVSTVL RVRSHLAPLW PFLGILAEII
360 370 380 390
ILVVIIVVYE KRKRPDEVPD AGPMKTNSTN NHKDKNLRQR NTN
Length:393
Mass (Da):43,932
Last modified:June 15, 2010 - v2
Checksum:iF11C6B9DF3A6D69A
GO
Isoform 1 (identifier: P97546-1) [UniParc]FASTAAdd to basket

Also known as: gp55, np55

The sequence of this isoform differs from the canonical sequence as follows:
     31-147: AGFVKSPMSE...AQATISVLQK → E
     370-370: D → DDDEP

Show »
Length:281
Mass (Da):31,292
Checksum:i92BFFB64844B211E
GO
Isoform 3 (identifier: P97546-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     31-147: AGFVKSPMSE...AQATISVLQK → E

Show »
Length:277
Mass (Da):30,836
Checksum:i898F4F38F138D7E4
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei31 – 147117AGFVK…SVLQK → E in isoform 1 and isoform 3. 2 PublicationsVSP_039258Add
BLAST
Alternative sequencei370 – 3701D → DDDEP in isoform 1. 1 PublicationVSP_039259

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99337 mRNA. Translation: CAA67711.1.
X99338 mRNA. Translation: CAA67712.1.
BC070947 mRNA. Translation: AAH70947.1.
RefSeqiNP_062253.1. NM_019380.1. [P97546-2]
XP_006243236.1. XM_006243174.2. [P97546-1]
XP_008764552.1. XM_008766330.1. [P97546-3]
UniGeneiRn.37476.

Genome annotation databases

EnsembliENSRNOT00000012091; ENSRNOP00000012091; ENSRNOG00000009029. [P97546-2]
ENSRNOT00000012295; ENSRNOP00000012295; ENSRNOG00000009029. [P97546-1]
GeneIDi56064.
KEGGirno:56064.
UCSCiRGD:620296. rat. [P97546-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99337 mRNA. Translation: CAA67711.1.
X99338 mRNA. Translation: CAA67712.1.
BC070947 mRNA. Translation: AAH70947.1.
RefSeqiNP_062253.1. NM_019380.1. [P97546-2]
XP_006243236.1. XM_006243174.2. [P97546-1]
XP_008764552.1. XM_008766330.1. [P97546-3]
UniGeneiRn.37476.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WV3X-ray1.95A148-333[»]
ProteinModelPortaliP97546.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000012091.

PTM databases

iPTMnetiP97546.
PhosphoSiteiP97546.
SwissPalmiP97546.
UniCarbKBiP97546.

Proteomic databases

PaxDbiP97546.
PRIDEiP97546.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000012091; ENSRNOP00000012091; ENSRNOG00000009029. [P97546-2]
ENSRNOT00000012295; ENSRNOP00000012295; ENSRNOG00000009029. [P97546-1]
GeneIDi56064.
KEGGirno:56064.
UCSCiRGD:620296. rat. [P97546-2]

Organism-specific databases

CTDi27020.
RGDi620296. Nptn.

Phylogenomic databases

eggNOGiENOG410IJET. Eukaryota.
ENOG4111V1Q. LUCA.
GeneTreeiENSGT00390000010516.
HOGENOMiHOG000263411.
HOVERGENiHBG008120.
InParanoidiP97546.
PhylomeDBiP97546.

Enzyme and pathway databases

ReactomeiR-RNO-112314. Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell.

Miscellaneous databases

EvolutionaryTraceiP97546.
PROiP97546.

Gene expression databases

ExpressionAtlasiP97546. baseline and differential.
GenevisibleiP97546. RN.

Family and domain databases

Gene3Di2.60.40.10. 3 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR027112. Neuroplastin.
IPR016243. Tyr_kinase_CSF1/PDGF_rcpt.
[Graphical view]
PANTHERiPTHR10075:SF5. PTHR10075:SF5. 1 hit.
PIRSFiPIRSF000615. TyrPK_CSF1-R. 1 hit.
SMARTiSM00409. IG. 3 hits.
SM00408. IGc2. 2 hits.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 3 hits.
PROSITEiPS50835. IG_LIKE. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Synaptic membrane glycoproteins gp65 and gp55 are new members of the immunoglobulin superfamily."
    Langnaese K., Beesley P.W., Gundelfinger E.D.
    J. Biol. Chem. 272:821-827(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, GLYCOSYLATION.
    Strain: Sprague-Dawley.
    Tissue: Brain.
  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 3).
    Tissue: Heart.
  3. Lubec G., Kang S.U., Lubec S.
    Submitted (SEP-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 150-159; 186-194; 209-226; 235-243; 245-271; 288-293 AND 363-379 (ISOFORM 1), IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Brain.
  4. "Isoform specific expression of the SDR-1 protein, alpha and beta in subregions of adult rodent brain."
    Lopez N.D., Kinoshita A., Taniwaki M., Tada H., Shirozu M., Nakano T., Tashiro K., Honjo T.
    Biomed. Res. 20:43-49(1999)
    Cited for: TISSUE SPECIFICITY.
  5. "The synaptic glycoprotein neuroplastin is involved in long-term potentiation at hippocampal CA1 synapses."
    Smalla K.H., Matthies H., Langnase K., Shabir S., Bockers T.M., Wyneken U., Staak S., Krug M., Beesley P.W., Gundelfinger E.D.
    Proc. Natl. Acad. Sci. U.S.A. 97:4327-4332(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (ISOFORM 2), SUBCELLULAR LOCATION (ISOFORM 2), TISSUE SPECIFICITY (ISOFORM 2).
  6. "The cell adhesion molecule neuroplastin-65 inhibits hippocampal long-term potentiation via a mitogen-activated protein kinase p38-dependent reduction in surface expression of GluR1-containing glutamate receptors."
    Empson R.M., Buckby L.E., Kraus M., Bates K.J., Crompton M.R., Gundelfinger E.D., Beesley P.W.
    J. Neurochem. 99:850-860(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (ISOFORM 2).
  7. "Neuroplastin-55 binds to and signals through the fibroblast growth factor receptor."
    Owczarek S., Kiryushko D., Larsen M.H., Kastrup J.S., Gajhede M., Sandi C., Berezin V., Bock E., Soroka V.
    FASEB J. 24:1139-1150(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 148-333 (ISOFORM 1), FUNCTION (ISOFORM 1), FGFR1-BINDING (ISOFORM 1), DISULFIDE BONDS, GLYCOSYLATION AT ASN-170; ASN-228; ASN-283 AND ASN-295.

Entry informationi

Entry nameiNPTN_RAT
AccessioniPrimary (citable) accession number: P97546
Secondary accession number(s): P97547, Q6IRE8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: June 15, 2010
Last modified: July 6, 2016
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.