User:Dreamer Wesley/N4BP2L2

NEDD4-binding protein 2-like 2 (N4BP2L2), also known as phosphonoformate immunoassociated protein 5 (PFAAP5), is a transcription factor or co-regulator. The gene of N4BP2L2 is found on minus strand of chromosome 13 in human. This gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat and chicken and its orthologs are found in 202 different organisms. There are two paralogs of N4BP2L2 in human. One is N4BP2 and another one is N4BP2L1.

Gene
N4BP2L2 is also called as PFAAP5, CG005, Protein from BRCA2 Region, 92M18.3 and CG016. It located on minus strand in chromosomal bind 13q13.1 and there are totally 22 exons found in N4BP2L2. The length of N4BP2L2 gene is 110294 base pairs (bp) from 32,432,417 to 32,542,710.

Transcript
There are more than 30 splicing isoforms of N4BP2L2 gene. Four of them are validated. The transcript coding the largest protein is N4BP2L2, transcript variant 4. It has 4301 bp. It is consisted of 10 exons (nucleotide 1-178, 179-1437, 1438-1562, 1563-1651, 1652=1728, 1729-1875, 1876-3614, 3615-3700, 3701-3745, 3746-4301).

Protein
There are four validated isoforms of N4BP2L2 protein. The longest one is the isoform 4. It is 1181 aa long. It has two special domains. The first one is AAA_33, also called AAA domain. Another one is NK (nucleoside/nucleotide kinase). NK domain is totally covered by AAA_33. N4BP2L2 is located in cell nucleus.

Protein composition
The molecular weight of N4BP2L2 isoform 4 is 136.9 KDa, and the isoeletric point is 6.51. The proportion of Alanine is extremely low and the proportion of Asparagine is little bit higher than the average protein appears in human.

There is a positive charge cluster from 564 to 591. Another high scored uncharged segment is from 268 to 331. There is neither high scoring hydrophobic segments nor high scoring transmembrane segments.

Secondary structure
In GOR, N4BP2L2 secondary structure predicted to contain random coils (c), alpha helix (h) and extended strand (e). An multiple sequence alignment of N4BP2L2 in Homo sapiens and its orthologs in Macaca fascicularis, Mus musculus, Monodelphis domestica was used to predict the conserved secondary structure of N4BP2L2 using Ali2D.

Tertiary structure
The tertiary structure is predicted by I-TASSER. The rank 1 identified structure analog by I-TASSER is Human Complement Factor H. The TM-score is 0.904 and coverage rate is 0.902. The red color indicates the N-terminus of N4BP2L2. And blue site indicates the C-terminus of the protein.

Expression
Based on expression part in NCBI gene database, N4BP2L2 is found high transcribed in endometrium, ovary, prostate, skin, thyroid, brain cerebellum. Highest expressed place of N4BP2L2 in brain is cortical subplate (CTXsp). Its raw expression value is 14.84. And the lowest expressed place of N4BP2L2 in brain is cerebellum (CB). Its raw expression value is 2.64.

Table 1. Ten lowest expressed tissue of N4BP2L2 ranked by count values

Table 2. Ten highest transcribed tissue of N4BP2L2 ranked by count values

Gene level regulation
The promoter region of N4BP2L2 transcript variant 4 is 1656 bp. Multiple transcription factors are predicted to bind with promoter or 5' UTR.

Table 3. 20 selected transcription factors for N4BP2L2 promoter predicted by genomatix

Transcript level regulation
Seven possible stem-loop structure are predicted in 3' UTR region.

Protein level regulation
120 sites are predicted by NetPhos, which can be phosphorylated. Position 23, a Cysteine, predicted to be palmitoylated. Position 8, a Glycine, is predicted to be N-myristolated. All results turn out that N4BP2L2 protein do not have signal peptide. The protein is predicted to have a 78.3% possible locating in nuclear.

Homologs / Evolution
The N4BP2L2 protein has two paralog in human. One is N4BP2, NEDD4-binding Protein 2. This protein has 17.4% identity and 27.9% similarity with homo sapiens N4BP2L2 protein. Another paralog is N4BP2L1, NEDD4-binding Protein 2-like 1. N4BP2L1 has 8.3% identity and 11.7% similarity with homo sapiens N4BP2L2 protein.

Currently, 202 orthologs of N4BP2L2 have been found. All of them are Chordata. The nearest orthologs are found in primates, such as crab-eating macaque. And the most distant orthologs can be found in fish, such as zebrafish, Australian ghostshark. The identity of these orthologs varies from 10% to more than 90% compared to homo sapiens N4BP2L2.

From the multiple sequence alignment (MSA) results of human N4BP2L2 protein and its orthologs, it is found that AAA domain is highly conserved in the whole evolution history.

Function and Clinic Significance
In neutrophils, N4BP2L2 is found to interact with transcription repressor Gfi1 and neutrophil elastase. It can adjust the cooperation of neutrophil elastase and Gfi1. Additionally, if this gene is silenced, the differentiation of Hematopoietic stem cell.

In clinic, N4BP2L2 was selected as one of "dose-responsive pharmacodynamic biomarkers for phase II clinical trials" of potent cyclin-dependent kinase inhibitor, R547. It is also reported that it can interact with the protein product of a oncogene, HPV18 E6.

Interacting Proteins
Searching in IntAct Molecular Interaction database for interacting proteins of N4BP2L2, it turns out 52 proteins. There proteins are from six organism: homo spaiens, Bacillus anthracis, Yersinia pestis, Hepatitis C virus, SARS coronavirus, Francisella tularensis. In human, the proteins in nuclear has a higher tendency to interact with N4BP2L2, such as Peptidyl-prolyl cis-trans isomerase H, Heterogeneous nuclear ribonucleoprotein M. Proteins which do not locate in nuclear may not interact with N4BP2L2 in vivo, such as Protein Wnt-16.

Table 4. Interacting protein of N4BP2L2 searched in IntAct

Suggested Reading

 * 1) Salipante, Stephen J., et al. “Contributions to Neutropenia from PFAAP5 (N4BP2L2), a Novel Protein Mediating Transcriptional Repressor Cooperation between Gfi1 and Neutrophil Elastase.” Molecular and Cellular Biology, vol. 29, no. 16, 2009, pp. 4394–4405., doi:10.1128/mcb.00596-09.