UniProtKB - Q8N300 (SVBP_HUMAN)
Protein
Small vasohibin-binding protein
Gene
SVBP
Organism
Homo sapiens (Human)
Status
Functioni
Enhances the tyrosine carboxypeptidase activity of VASH1 and VASH2, thereby promoting the removal of the C-terminal tyrosine residue of alpha-tubulin (PubMed:29146869, PubMed:31270470, PubMed:31235911, PubMed:31324789, PubMed:31171830, PubMed:31235910). This activity is critical for spindle function and accurate chromosome segregation during mitosis since microtuble detyronisation regulates mitotic spindle length and postioning (PubMed:31171830). Also required to enhance the solubility and secretion of VASH1 and VASH2 (PubMed:20736312, PubMed:27879017, PubMed:30607023). Plays a role in axon and excitatory synapse formation (PubMed:31235911).9 Publications
GO - Molecular functioni
- microtubule binding Source: UniProtKB
GO - Biological processi
- axon development Source: UniProtKB
- negative regulation of endothelial cell migration Source: MGI
- negative regulation of protein ubiquitination Source: MGI
- protein secretion Source: MGI
- proteolysis Source: UniProtKB
- regulation of metallopeptidase activity Source: UniProtKB
Enzyme and pathway databases
PathwayCommonsi | Q8N300 |
Reactomei | R-HSA-8955332, Carboxyterminal post-translational modifications of tubulin |
Names & Taxonomyi
Protein namesi | Recommended name: Small vasohibin-binding protein1 PublicationAlternative name(s): Coiled coil domain-containing protein 23Imported |
Gene namesi | |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:29204, SVBP |
MIMi | 617853, gene |
neXtProti | NX_Q8N300 |
VEuPathDBi | HostDB:ENSG00000177868.11 |
Subcellular locationi
Cytoplasm and Cytosol
- Cytoplasm By similarity
Extracellular region or secreted
- Secreted By similarity
Cytoskeleton
- cytoskeleton 1 Publication
Note: Detected both intracellularly and extracellularly (By similarity). Within cells, localizes mainly to the apical part of the cell (By similarity).By similarity
Cytoskeleton
- cytoskeleton Source: UniProtKB-SubCell
Extracellular region or secreted
- extracellular region Source: UniProtKB-SubCell
Other locations
- apical part of cell Source: MGI
- cytoplasm Source: UniProtKB-SubCell
Keywords - Cellular componenti
Cytoplasm, Cytoskeleton, SecretedPathology & Biotechi
Involvement in diseasei
Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly (NEDAHM)1 Publication
The disease is caused by variants affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive neurodevelopmental disorder characterized by intellectual disability, microcephaly, ataxia, and muscular hypotonia.
Related information in OMIMFeature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_083027 | 28 – 66 | Missing in NEDAHM; probably not expressed at protein level; impaired VASH1 secretion and solubility. 1 PublicationAdd BLAST | 39 |
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 32 | K → E: Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 34 | R → E: No effect on VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 35 – 36 | QR → AA: Strongly decreased interaction with VASH1. Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. Strongly decreased interaction with VASH2. Decreased VASH2 tyrosine carboxypeptidase activity on alpha-tubulin. 2 Publications | 2 | |
Mutagenesisi | 35 | Q → A: Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 36 | R → E: Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 39 – 42 | IYAL → EALE: Strongly decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 4 | |
Mutagenesisi | 39 – 40 | IY → AA: Strongly decreased interaction with VASH1. Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. Disrupted interaction with VASH2. Decreased VASH2 tyrosine carboxypeptidase activity on alpha-tubulin. 2 Publications | 2 | |
Mutagenesisi | 39 | I → E: No effect on VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 40 | Y → F: No effect on VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 42 – 43 | LN → AA: Decreased interaction with VASH1. Almost abolished VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. Strongly decreased interaction with VASH2. Decreased VASH2 tyrosine carboxypeptidase activity on alpha-tubulin. 2 Publications | 2 | |
Mutagenesisi | 42 | L → E: No effect on VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 43 | N → A: Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 45 – 46 | VM → AA: Slightly decreased interaction with VASH1. Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. No effect on interaction with VASH2. No effect on VASH2 tyrosine carboxypeptidase activity on alpha-tubulin. 2 Publications | 2 | |
Mutagenesisi | 47 | T → D: Decreased VASH1 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 1 | |
Mutagenesisi | 50 – 54 | EQQQF → AQQQA: No effect on interaction with VASH2. No effect on VASH2 tyrosine carboxypeptidase activity on alpha-tubulin. 1 Publication | 5 |
Keywords - Diseasei
Disease variant, Mental retardationOrganism-specific databases
DisGeNETi | 374969 |
MalaCardsi | SVBP |
MIMi | 618569, phenotype |
OpenTargetsi | ENSG00000177868 |
Orphaneti | 528084, Non-specific syndromic intellectual disability |
PharmGKBi | PA142672181 |
Miscellaneous databases
Pharosi | Q8N300, Tdark |
Genetic variation databases
BioMutai | SVBP |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000233663 | 1 – 66 | Small vasohibin-binding proteinAdd BLAST | 66 |
Proteomic databases
EPDi | Q8N300 |
jPOSTi | Q8N300 |
MassIVEi | Q8N300 |
MaxQBi | Q8N300 |
PaxDbi | Q8N300 |
PeptideAtlasi | Q8N300 |
PRIDEi | Q8N300 |
ProteomicsDBi | 71745 |
PTM databases
iPTMneti | Q8N300 |
MetOSitei | Q8N300 |
PhosphoSitePlusi | Q8N300 |
Expressioni
Gene expression databases
Bgeei | ENSG00000177868, Expressed in cortical plate and 206 other tissues |
Genevisiblei | Q8N300, HS |
Organism-specific databases
HPAi | ENSG00000177868, Low tissue specificity |
Interactioni
Subunit structurei
Interacts with VASH1 and VASH2.
8 PublicationsBinary interactionsi
Q8N300
With | #Exp. | IntAct |
---|---|---|
VASH1 - isoform 1 [Q7L8A9-1] | 2 | EBI-21497577,EBI-21497569 |
GO - Molecular functioni
- microtubule binding Source: UniProtKB
Protein-protein interaction databases
BioGRIDi | 131942, 1 interactor |
IntActi | Q8N300, 1 interactor |
STRINGi | 9606.ENSP00000361599 |
Miscellaneous databases
RNActi | Q8N300, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q8N300 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Coiled coil
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Coiled coili | 5 – 52 | Sequence analysisAdd BLAST | 48 |
Sequence similaritiesi
Belongs to the SVBP family.Curated
Keywords - Domaini
Coiled coilPhylogenomic databases
eggNOGi | ENOG502S99I, Eukaryota |
GeneTreei | ENSGT00390000006113 |
HOGENOMi | CLU_2830589_0_0_1 |
InParanoidi | Q8N300 |
OMAi | AMDPPAR |
OrthoDBi | 1606567at2759 |
PhylomeDBi | Q8N300 |
TreeFami | TF344015 |
Family and domain databases
InterProi | View protein in InterPro IPR031378, SVBP |
PANTHERi | PTHR34762, PTHR34762, 1 hit |
Pfami | View protein in Pfam PF15674, CCDC23, 1 hit |
i Sequence
Sequence statusi: Complete.
Q8N300-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MDPPARKEKT KVKESVSRVE KAKQKSAQQE LKQRQRAEIY ALNRVMTELE
60
QQQFDEFCKQ MQPPGE
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_083027 | 28 – 66 | Missing in NEDAHM; probably not expressed at protein level; impaired VASH1 secretion and solubility. 1 PublicationAdd BLAST | 39 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK291356 mRNA Translation: BAF84045.1 AC098484 Genomic DNA No translation available. AL512353 Genomic DNA No translation available. CH471059 Genomic DNA Translation: EAX07134.1 CH471059 Genomic DNA Translation: EAX07135.1 BC029427 mRNA Translation: AAH29427.1 |
CCDSi | CCDS474.1 |
RefSeqi | NP_955374.1, NM_199342.3 XP_016856715.1, XM_017001226.1 |
Genome annotation databases
Ensembli | ENST00000372521; ENSP00000361599; ENSG00000177868 ENST00000372522; ENSP00000361600; ENSG00000177868 |
GeneIDi | 374969 |
KEGGi | hsa:374969 |
UCSCi | uc001cib.3, human |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK291356 mRNA Translation: BAF84045.1 AC098484 Genomic DNA No translation available. AL512353 Genomic DNA No translation available. CH471059 Genomic DNA Translation: EAX07134.1 CH471059 Genomic DNA Translation: EAX07135.1 BC029427 mRNA Translation: AAH29427.1 |
CCDSi | CCDS474.1 |
RefSeqi | NP_955374.1, NM_199342.3 XP_016856715.1, XM_017001226.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
6J4O | X-ray | 2.30 | B | 1-66 | [»] | |
6J4P | X-ray | 1.60 | B | 1-66 | [»] | |
6J4Q | X-ray | 2.70 | B/D/G/K | 1-66 | [»] | |
6J4S | X-ray | 2.80 | B | 1-66 | [»] | |
6J4U | X-ray | 2.00 | B | 1-66 | [»] | |
6J4V | X-ray | 2.10 | B | 1-66 | [»] | |
6J7B | X-ray | 1.62 | B | 1-52 | [»] | |
6J8F | X-ray | 2.28 | A | 3-48 | [»] | |
6J8N | X-ray | 1.95 | A/C | 1-66 | [»] | |
6J8O | X-ray | 1.85 | A | 3-49 | [»] | |
6J91 | X-ray | 3.50 | A | 1-66 | [»] | |
6J9H | X-ray | 2.31 | A/C | 1-66 | [»] | |
6JZC | X-ray | 2.20 | C/D | 1-66 | [»] | |
6JZD | X-ray | 2.48 | B | 1-66 | [»] | |
6JZE | X-ray | 2.51 | B | 1-66 | [»] | |
6K81 | X-ray | 2.28 | B | 1-66 | [»] | |
6LPG | X-ray | 2.30 | B | 2-66 | [»] | |
6NVQ | X-ray | 2.10 | B | 1-66 | [»] | |
6OCF | X-ray | 2.10 | B | 18-66 | [»] | |
6OCG | X-ray | 1.83 | B | 26-51 | [»] | |
6OCH | X-ray | 2.00 | B/D | 25-52 | [»] | |
6QBY | X-ray | 2.09 | B/D | 1-66 | [»] | |
6WSL | electron microscopy | 3.10 | D/H | 1-66 | [»] | |
SMRi | Q8N300 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 131942, 1 interactor |
IntActi | Q8N300, 1 interactor |
STRINGi | 9606.ENSP00000361599 |
PTM databases
iPTMneti | Q8N300 |
MetOSitei | Q8N300 |
PhosphoSitePlusi | Q8N300 |
Genetic variation databases
BioMutai | SVBP |
Proteomic databases
EPDi | Q8N300 |
jPOSTi | Q8N300 |
MassIVEi | Q8N300 |
MaxQBi | Q8N300 |
PaxDbi | Q8N300 |
PeptideAtlasi | Q8N300 |
PRIDEi | Q8N300 |
ProteomicsDBi | 71745 |
Protocols and materials databases
Antibodypediai | 2034, 57 antibodies |
Genome annotation databases
Ensembli | ENST00000372521; ENSP00000361599; ENSG00000177868 ENST00000372522; ENSP00000361600; ENSG00000177868 |
GeneIDi | 374969 |
KEGGi | hsa:374969 |
UCSCi | uc001cib.3, human |
Organism-specific databases
CTDi | 374969 |
DisGeNETi | 374969 |
GeneCardsi | SVBP |
HGNCi | HGNC:29204, SVBP |
HPAi | ENSG00000177868, Low tissue specificity |
MalaCardsi | SVBP |
MIMi | 617853, gene 618569, phenotype |
neXtProti | NX_Q8N300 |
OpenTargetsi | ENSG00000177868 |
Orphaneti | 528084, Non-specific syndromic intellectual disability |
PharmGKBi | PA142672181 |
VEuPathDBi | HostDB:ENSG00000177868.11 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | ENOG502S99I, Eukaryota |
GeneTreei | ENSGT00390000006113 |
HOGENOMi | CLU_2830589_0_0_1 |
InParanoidi | Q8N300 |
OMAi | AMDPPAR |
OrthoDBi | 1606567at2759 |
PhylomeDBi | Q8N300 |
TreeFami | TF344015 |
Enzyme and pathway databases
PathwayCommonsi | Q8N300 |
Reactomei | R-HSA-8955332, Carboxyterminal post-translational modifications of tubulin |
Miscellaneous databases
BioGRID-ORCSi | 374969, 148 hits in 979 CRISPR screens |
ChiTaRSi | SVBP, human |
GenomeRNAii | 374969 |
Pharosi | Q8N300, Tdark |
PROi | PR:Q8N300 |
RNActi | Q8N300, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000177868, Expressed in cortical plate and 206 other tissues |
Genevisiblei | Q8N300, HS |
Family and domain databases
InterProi | View protein in InterPro IPR031378, SVBP |
PANTHERi | PTHR34762, PTHR34762, 1 hit |
Pfami | View protein in Pfam PF15674, CCDC23, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | SVBP_HUMAN | |
Accessioni | Q8N300Primary (citable) accession number: Q8N300 Secondary accession number(s): A8K5P1, D3DPW7 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | May 2, 2006 |
Last sequence update: | October 1, 2002 | |
Last modified: | April 7, 2021 | |
This is version 119 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Human chromosome 1
Human chromosome 1: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families