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N4BP2 NEDD4 binding protein 2 [ Homo sapiens (human) ]

Gene ID: 55728, updated on 3-Apr-2024

Summary

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Official Symbol
N4BP2provided by HGNC
Official Full Name
NEDD4 binding protein 2provided by HGNC
Primary source
HGNC:HGNC:29851
See related
Ensembl:ENSG00000078177 MIM:619139; AllianceGenome:HGNC:29851
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
B3BP
Summary
This gene encodes a protein containing a polynucleotide kinase domain (PNK) near the N-terminal region, and a Small MutS Related (Smr) domain near the C-terminal region. The encoded protein can bind to both B-cell leukemia/lymphoma 3 (BCL-3) and neural precursor cell expressed, developmentally downregulated 4, (Nedd4) proteins. This protein binds and hydrolyzes ATP, may function as a 5'-polynucleotide kinase, and has the capacity to be a ubiquitylation substrate. This protein may play a role in transcription-coupled DNA repair or genetic recombination. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in thyroid (RPKM 3.3), lymph node (RPKM 2.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4p14
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (40056850..40190470)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (40026953..40157597)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (40058470..40159872)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene PDS5 cohesin associated factor A Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:39977870-39978778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:39991585-39992282 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:40000455-40000959 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40001597-40002110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40002111-40002626 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40002627-40003140 Neighboring gene poly(A) binding protein cytoplasmic 1 pseudogene 1 Neighboring gene keratin 18 pseudogene 25 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21472 Neighboring gene acyl-CoA thioesterase 7 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:40070175-40070676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:40070677-40071176 Neighboring gene uncharacterized LOC124900183 Neighboring gene RNA, U6 small nuclear 1112, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40140819-40141412 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40149211-40149992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21473 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40239787-40240778 Neighboring gene ras homolog family member H Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:40252200-40253399 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:40259652-40260430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40270986-40271804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40271805-40272621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21487 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:40311945-40313144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:40318591-40319429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21489 Neighboring gene long intergenic non-protein coding RNA 2265

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Modulated nicking endonuclease function by the N-terminal extended region of the smr domain in human Bcl-3 binding protein. Jeong EY, et al. Proteins, 2012 Jan. PMID 22072629
  2. Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain. Diercks T, et al. J Mol Biol, 2008 Nov 28. PMID 18804481
  3. Haplotype of gene Nedd4 binding protein 2 associated with sporadic nasopharyngeal carcinoma in the Southern Chinese population. Zheng MZ, et al. J Transl Med, 2007 Jul 13. PMID 17626640, Free PMC Article
  4. Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate. Leslie EJ, et al. Am J Med Genet A, 2017 Jun. PMID 28425186, Free PMC Article
  5. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Lee MG, et al. Science, 2007 Oct 19. PMID 17761849

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. We found that a burden of low-frequency coding variants in N4BP2, CDSN, PRTG, and AHRR were associated with increased risk of Nonsyndromic cleft lip with or without cleft palate (NSCL/P) . Low-frequency variants in other genes were associated with decreased risk of NSCL/P. These results demonstrate that low-frequency variants contribute to the genetic etiology of NSCL/P
    Title: Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate.
  2. the N-terminal extended region of the Smr domain in the native B3bp may function as a regulatory region for the nicking endonuclease
    Title: Modulated nicking endonuclease function by the N-terminal extended region of the smr domain in human Bcl-3 binding protein.
  3. These data suggest that haplotype blocks ATTA and GTTG of N4BP2 is correlation with the risk of sporadic nasopharyngeal carcinoma in the Southern Chinese population.
    Title: Haplotype of gene Nedd4 binding protein 2 associated with sporadic nasopharyngeal carcinoma in the Southern Chinese population.
  4. The solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins, is determined.
    Title: Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain.
  5. B3BP is a 5'-polynucleotide kinase
    Title: Identification and characterization of BCL-3-binding protein: implications for transcription and DNA repair or recombination.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10680, KIAA1413

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables endonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
NEDD4-binding protein 2
Names
BCL-3-binding protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001318359.2 → NP_001305288.1  NEDD4-binding protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (2) that has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AB371584, AC095057, AC098591, AK001542, AU129951, AW135590
    UniProtKB/TrEMBL
    B2ZZ87
    Conserved Domains (3) summary
    smart00463
    Location:1608 → 1690
    SMR; Small MutS-related domain
    pfam08590
    Location:1541 → 1600
    DUF1771; Domain of unknown function (DUF1771)
    pfam13671
    Location:369 → 495
    AAA_33; AAA domain

  2. NM_018177.6 → NP_060647.2  NEDD4-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_060647.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AB371584, AC095057, AC098591, AK001542, AW135590, BC126466
    Consensus CDS
    CCDS3457.1
    UniProtKB/Swiss-Prot
    A0AVR3, Q86UW6, Q9NVK2, Q9P2D4
    UniProtKB/TrEMBL
    B2ZZ87
    Related
    ENSP00000261435.6, ENST00000261435.11
    Conserved Domains (4) summary
    smart00463
    Location:1688 → 1770
    SMR; Small MutS-related domain
    cd14365
    Location:47 → 87
    CUE_N4BP2; CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins
    pfam08590
    Location:1621 → 1680
    DUF1771; Domain of unknown function (DUF1771)
    pfam13671
    Location:449 → 575
    AAA_33; AAA domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    40056850..40190470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513716.3 → XP_011512018.2  NEDD4-binding protein 2 isoform X1

  2. XM_047415953.1 → XP_047271909.1  NEDD4-binding protein 2 isoform X2

    Related
    ENSP00000426430.1, ENST00000513269.1

  3. XM_047415954.1 → XP_047271910.1  NEDD4-binding protein 2 isoform X3

    UniProtKB/Swiss-Prot
    A0AVR3, Q86UW6, Q9NVK2, Q9P2D4

  4. XM_047415955.1 → XP_047271911.1  NEDD4-binding protein 2 isoform X4

  5. XM_047415957.1 → XP_047271913.1  NEDD4-binding protein 2 isoform X1

  6. XM_047415956.1 → XP_047271912.1  NEDD4-binding protein 2 isoform X1

  7. XM_017008398.1 → XP_016863887.1  NEDD4-binding protein 2 isoform X3

    UniProtKB/Swiss-Prot
    A0AVR3, Q86UW6, Q9NVK2, Q9P2D4
    UniProtKB/TrEMBL
    B2ZZ87
    Conserved Domains (4) summary
    smart00463
    Location:1688 → 1770
    SMR; Small MutS-related domain
    cd14365
    Location:47 → 87
    CUE_N4BP2; CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins
    pfam08590
    Location:1621 → 1680
    DUF1771; Domain of unknown function (DUF1771)
    pfam13671
    Location:449 → 575
    AAA_33; AAA domain

  8. XM_011513720.1 → XP_011512022.1  NEDD4-binding protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011512022.1

    UniProtKB/TrEMBL
    B2ZZ87
    Conserved Domains (3) summary
    smart00463
    Location:1608 → 1690
    SMR; Small MutS-related domain
    pfam08590
    Location:1541 → 1600
    DUF1771; Domain of unknown function (DUF1771)
    pfam13671
    Location:369 → 495
    AAA_33; AAA domain

  9. XM_011513721.1 → XP_011512023.1  NEDD4-binding protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011512023.1

    UniProtKB/TrEMBL
    B2ZZ87
    Conserved Domains (3) summary
    smart00463
    Location:1608 → 1690
    SMR; Small MutS-related domain
    pfam08590
    Location:1541 → 1600
    DUF1771; Domain of unknown function (DUF1771)
    pfam13671
    Location:369 → 495
    AAA_33; AAA domain

RNA

  1. XR_007057942.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    40026953..40157597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350479.1 → XP_054206454.1  NEDD4-binding protein 2 isoform X2

  2. XM_054350477.1 → XP_054206452.1  NEDD4-binding protein 2 isoform X1

  3. XM_054350476.1 → XP_054206451.1  NEDD4-binding protein 2 isoform X1

  4. XM_054350478.1 → XP_054206453.1  NEDD4-binding protein 2 isoform X2

  5. XM_054350480.1 → XP_054206455.1  NEDD4-binding protein 2 isoform X3

    UniProtKB/Swiss-Prot
    A0AVR3, Q86UW6, Q9NVK2, Q9P2D4

  6. XM_054350482.1 → XP_054206457.1  NEDD4-binding protein 2 isoform X4

  7. XM_054350485.1 → XP_054206460.1  NEDD4-binding protein 2 isoform X1

  8. XM_054350483.1 → XP_054206458.1  NEDD4-binding protein 2 isoform X1

  9. XM_054350481.1 → XP_054206456.1  NEDD4-binding protein 2 isoform X3

    UniProtKB/Swiss-Prot
    A0AVR3, Q86UW6, Q9NVK2, Q9P2D4

  10. XM_054350484.1 → XP_054206459.1  NEDD4-binding protein 2 isoform X1

  11. XM_054350486.1 → XP_054206461.1  NEDD4-binding protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86UW6.2 GenPept UniProtKB/Swiss-Prot:Q86UW6

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