Protein:PDXK |
Protein Summary |
 Gene summary |
| Gene name: PDXK | ASpdb.0 ID: 8566 | Gene | Gene symbol | PDXK | Gene ID | 8566 |
| Gene name | pyridoxal kinase |
| Synonyms | C21orf124|C21orf97|HEL-S-1a|HMSN6C|PKH|PNK|PRED79 |
| Cytomap | 21q22.3 |
| Type of gene | protein-coding |
| Description | pyridoxal kinaseepididymis secretory sperm binding protein Li 1apyridoxal (pyridoxine, vitamin B6) kinasepyridoxamine kinasepyridoxine kinasevitamin B6 kinase |
| Modification date | 20240305 |
| UniProtAcc | O00764 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PDXK | GO:0000287 | magnesium ion binding | 17766369 |
| Gene | PDXK | GO:0005524 | ATP binding | 16600635|17766369 |
| Gene | PDXK | GO:0005654 | nucleoplasm | - |
| Gene | PDXK | GO:0008270 | zinc ion binding | 10987144 |
| Gene | PDXK | GO:0008478 | pyridoxal kinase activity | 9099727|10987144|17766369 |
| Gene | PDXK | GO:0009443 | pyridoxal 5'-phosphate salvage | 9099727|10987144|17766369 |
| Gene | PDXK | GO:0030170 | pyridoxal phosphate binding | 16600635 |
| Gene | PDXK | GO:0030955 | potassium ion binding | 9252787|17766369 |
| Gene | PDXK | GO:0031402 | sodium ion binding | 9252787|17766369 |
| Gene | PDXK | GO:0031403 | lithium ion binding | 9252787 |
| Gene | PDXK | GO:0042803 | protein homodimerization activity | 16600635|17766369 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| O00764-1 | O00764-1_2f7k_A.pdb | 2F7K | X-ray | 2.8 | A | 1 | 312 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| O00764 | PDXK | O00764-1 | O00764-2 | 312 | 284 | 83 | 110 | Deletion | none | none | 82 | 82 |
| O00764 | PDXK | O00764-1 | O00764-3 | 312 | 239 | 1 | 73 | Deletion | none | none | 0 | 0 |
| Multiple sequence alignment of our canonical and alternatively spliced PDXK |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PDXK |
| UniProt-id | ENSG | ENST | ENSP |
| O00764-1 | ENSG00000160209.19 | ENST00000291565.9 | ENSP00000291565.4 |
| O00764-2 | ENSG00000160209.19 | ENST00000468090.5 | ENSP00000418359.1 |
| UniProt-id | NM ID | NP ID |
| O00764-1 | NM_003681.4 | NP_003672.1 |
| O00764-3 | XM_005261199.2 | XP_005261256.1 |
| O00764-3 | XM_011529761.1 | XP_011528063.1 |
| Amino acid sequences of our canonical and alternatively spliced PDXK |
| accession_id | Protein sequence |
| O00764-1 | MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTGYTRDKSF LAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGP DTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRT |
| O00764-2 | MEEECRVLSIQSHVIRGYVGNRAATFPLQVLGFEIDAVNSVQFSNHTGYAHWKGQVLNSDELQELYEGLRLNNMNKYDYVLTVCDPVLGD KWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIHSQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRR NPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLKVACEKTVSTLHHVLQRTIQCAKAQAGEGVRPSPMQLELRMVQSKR |
| O00764-3 | MNKYDYVLTGYTRDKSFLAMVVDIVQELKQQNPRLVYVCDPVLGDKWDGEGSMYVPEDLLPVYKEKVVPLADIITPNQFEAELLSGRKIH SQEEALRVMDMLHSMGPDTVVITSSDLPSPQGSNYLIVLGSQRRRNPAGSVVMERIRMDIRKVDAVFVGTGDLFAAMLLAWTHKHPNNLK |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PDXK (go to UniProt):O00764 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
Gene Isoform Structures and Expression Levels for PDXK |
| Gene structures of our canonical and alternative spliced genes of PDXK * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of O00764-1 |
| 3D view using mol* of O00764-2 |
| 3D view using mol* of O00764-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of O00764-1 |
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| pLDDT distribution across the protein length of O00764-2 |
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| pLDDT distribution across the protein length of O00764-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of O00764-1 |
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| Ramachandran plot of O00764-2 |
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| Ramachandran plot of O00764-3 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| O00764-1 | 1.057 | 333 | 1.06 | 859.901 | 0.447 | 0.784 | 0.992 | 0.945 | 1.075 | 0.879 | 0.654 | 11,12,13,14,19,20,41,43,46,47,48,83,84,113,115,118 ,119,120,121,122,127,148,150,151,152,153,186,187,1 88,189,198,199,201,223,224,225,226,228,229,230,231 ,232,233,234,235,237,260,263,264,267,268,283,284,2 86,289,290,307 |
| O00764-2 | 1.048 | 281 | 1.076 | 1248.863 | 0.577 | 0.745 | 0.936 | 0.841 | 0.955 | 0.881 | 1.035 | 10,11,12,13,14,19,20,41,43,46,47,48,82,83,85,87,89 ,90,91,92,93,94,99,120,122,123,124,125,158,159,160 ,161,171,173,195,196,197,198,199,200,201,202,203,2 04,205,206,207,209,232,235,236,239,240,243,247,251 ,253,254,255,256,258,261,262 |
| O00764-3 | 1.072 | 200 | 0.982 | 661.99 | 0.435 | 0.805 | 1.046 | 0.748 | 1.353 | 0.553 | 0.829 | 11,40,42,45,46,47,48,49,54,75,76,77,78,79,80,113,1 14,115,116,126,128,150,151,152,153,155,156,157,158 ,159,160,161,162,164,187,190,191,194,195 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of O00764-1_O00764-1_2f7k_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O00764-1_2f7k_A_O00764-2.pdb |
| 3D view using mol* of O00764-1_2f7k_A_O00764-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of O00764-1_O00764-2.pdb |
| 3D view using mol* of O00764-1_O00764-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/O00764-1_vs_O00764-2.png |
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| ./stats/secondary_structure/figure/O00764-1_vs_O00764-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/O00764-1_vs_O00764-2.png |
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| ./stats/relative_asa/O00764-1_vs_O00764-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to PDXK |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| O00764 | PDXK | DB00147 | Pyridoxal | experimental, nutraceutical | |
| O00764 | PDXK | DB03909 | Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate | experimental | |
| O00764 | PDXK | DB00165 | Pyridoxine | approved, investigational, nutraceutical, vet_approved | ligand |
| O00764 | PDXK | DB04770 | O6-(R)-ROSCOVITINE, R-2-(6-BENZYLOXY-9-ISOPROPYL-9H-PURIN-2-YLAMINO)-BUTAN-1-OL | experimental | |
| O00764 | PDXK | DB04776 | (2R)-2-({6-[benzyl(methyl)amino]-9-isopropyl-9H-purin-2-yl}amino)butan-1-ol | experimental |
Related Diseases to PDXK |
| Previous studies relating to the alternative splicing of PDXK and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PDXK | 21697133 | Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. | PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. | D019572 | Retinal Neoplasms |
| PDXK | 21697133 | Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. | PURPOSE. To collect an entire set of full-length cDNA clones derived from human retina-derived cell lines and to identify full-length transcripts for retinal preferentially expressed genes. METHODS. The full-length cDNA libraries were constructed from a retinoblastoma cell line, Y79, and a retinal pigment epithelium cell line, ARPE-19, using the vector-capping method, which generates a genuine full-length cDNA. By single-pass sequencing of the 5'-end of cDNA clones and subsequent mapping to the human genome, the authors determined their transcriptional start sites and annotated the cDNA clones. RESULTS. Of the 23,616 clones isolated from Y79-derived cDNA libraries, 19,229 full-length cDNA clones were identified and classified into 4808 genes, including genes of >10 kbp. Of the 7067 genes obtained from the Y79 and ARPE-19 libraries, the authors selected 72 genes that were preferentially expressed in the eye, of which 131 clones corresponding to 57 genes were fully sequenced. As a result, we discovered many variants that were produced by different transcriptional start sites, alternative splicing, and alternative polyadenylation. CONCLUSIONS. The bias-free, full-length cDNA libraries constructed using the vector-capping method were shown to be useful for collecting an entire set of full-length cDNA clones for these retinal cell lines. Full-length transcriptome analysis of these cDNA libraries revealed that there were, unexpectedly, many transcript variants for each gene, indicating that obtaining the full-length cDNA for each variant is indispensable for analyzing its function. The full-length cDNA clones (approximately 80,000 clones each for ARPE-19 and Y79) will be useful as a resource for investigating the human retina. | D012175 | Retinoblastoma |
Clinically important variants in PDXK |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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