Neuroblastoma breakpoint family, member 3, also known as NBPF3, is a human gene of the neuroblastoma breakpoint family, which resides on chromosome 1 of the human genome. NBPF3 is located at 1p36.12, immediately upstream of genes ALPL and RAP1GAP.
Protein sequence
The NBPF3 gene is 633 amino acids long and contains five DUF1220 domains, which are highlighted in the image below. DUF1220 domains are found in all other members of the neuroblastoma breakpoint family. The protein has a very repetitive structure, since, along with the remaining members of its protein family, it likely arose form segmental duplications on chromosome 1.
The domains are located at residues 236–298, 322–385, 394–460, 469–535, and 544–610.
The protein sequence is rich in three amino acids that are polar and negatively charged at physiological pH: glutamic acid, aspartic acid and glutamine. The isoelectric point of the protein is 4.21, the acidity of which may be attributed to the abundance of these amino acids.
Isoforms and sequence characteristics
There are four known isoforms of the NPBF3 gene. While isoform 1 is the dominant form of the gene, each other isoform has unique changes to the protein sequence that may affect the structure, expression or function of the gene product:
Isoform Sequence Omissions Sequence Additions Length 1--633 21-56-577 3350-386331 R→RSSGRFCCLISVGYIFCHPCPAWLIR621 41-358-275
These isoforms are represented in the following schematic, along with additional sequence characteristics which include Poly-Glu compositional biases and a potential coiled coil.
Function
The function of the neuroblastoma breakpoint family proteins, including NPBF3, is not yet understood by the scientific community. Because of the repetitive composition of this family of genes as well as their amplification in primates, it has been suggested that the family is involved in cognitive development and the evolution of primates.
It has also been suggested that there is a connection between the neuroblastoma breakpoint family and oncogenesis. Due to the up-regulation of NBPF genes in some tumor tissues, proteins of this family have been hypothesized to be oncogenes. It has also been suggested that members of the neuroblastoma breakpoint family are tumor suppressor genes, due to a loss of heterozygosity in tumor tissue in the region of chromosome 1 where NBPF3 and other NBPF proteins are located.
Homology
Orthologs of NBPF3 are found primarily in primate species, though orthologous sequences can be found in cow, horse, and dog species. There is no mouse ortholog of NPBF3.
Species Organism common name NCBI accession Sequence identity Sequence similarity Length (AAs) Number of DUF1220 domains Homo sapiensHumanCAB66824100%100%6335 Pan troglodytesChimpanzeeXP_001163311.196%98%6335 Macaca mulattaRhesus macaqueXP_001114167.155%65%6204 Pongo albeliiOrangutanNP_001127345.189%93%2023 Bos taurusCowXP_611707.433%49%8164 Equus caballusHorseXP_001916030.137%55%10370 Canis lupus familiarisDogXP_540269.240%59%1760
NPBF3 has many human paralogs because it is a member of a gene family.
Species Gene name NCBI accession Sequence identity Sequence similarity Length (AAs) Homo sapiensNBPF3CAB66824100%100%633 Homo sapiensNBPF10NP_001034792.277%83%867 Homo sapiensNBPF1NP_060410.275%83%1214 Homo sapiensNBPF20NP_001032764.175%84%942 Homo sapiensNBPF8XP_001726998.175%84%3815 Homo sapiensNBPF16NP_001096133.175%84%670 Homo sapiensNBPF15NP_775909.175%84%670 Homo sapiensNBPF11NP_899228.375%83%790 Homo sapiensNBPF14NP_056198.174%83%921 Homo sapiensNBPF9XP_001717450.180%88%687 Homo sapiensNBPF7NP_001041445.169%79%421 Homo sapiensNBPF6NP_001137459.154%68%667 Homo sapiensNBPF4NP_001137461.153%67%638 Homo sapiensNBPF12XP_001715862.155%63%427 Homo sapiensNBPF5XP_001714524.160%73%428
Both orthologs and paralogs of NBPF3 were found using the databases BLAT. and BLAST
Protein interactions
NPBF3 interacts with three other proteins: C1orf19, ankyrin-1 (ANK1) and Ewing sarcoma breakpoint region 1 (EWSR1). It is not known how these proteins interact or what the product of these interactions may be.
References
Further reading