Protein:PANK2 |
Protein Summary |
 Gene summary |
| Gene name: PANK2 | ASpdb.0 ID: 80025 | Gene | Gene symbol | PANK2 | Gene ID | 80025 |
| Gene name | pantothenate kinase 2 |
| Synonyms | C20orf48|HARP|HSS|NBIA1|PKAN |
| Cytomap | 20p13 |
| Type of gene | protein-coding |
| Description | pantothenate kinase 2, mitochondrialHallervorden-Spatz syndromepantothenate kinase-associated neurodegenerationpantothenic acid kinase 2 |
| Modification date | 20240323 |
| UniProtAcc | Q9BZ23 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | PANK2 | GO:0005634 | nucleus | 23152917 |
| Gene | PANK2 | GO:0005739 | mitochondrion | 15659606|23152917 |
| Gene | PANK2 | GO:0005758 | mitochondrial intermembrane space | 23152917 |
| Gene | PANK2 | GO:0005829 | cytosol | - |
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 |
| Q9BZ23-1 | Q9BZ23-1_5e26_B.pdb | 5E26 | X-ray | 2.14 | B | 207 | 568 |
| 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 |
| Q9BZ23 | PANK2 | Q9BZ23-1 | Q9BZ23-2 | 570 | 279 | 1 | 291 | Deletion | none | none | 0 | 0 |
| Q9BZ23 | PANK2 | Q9BZ23-1 | Q9BZ23-3 | 570 | 447 | 1 | 123 | Deletion | none | none | 0 | 0 |
| Q9BZ23 | PANK2 | Q9BZ23-1 | Q9BZ23-4 | 570 | 460 | 1 | 110 | Deletion | none | none | 0 | 0 |
| Q9BZ23 | PANK2 | Q9BZ23-1 | Q9BZ23-4 | 570 | 460 | 111 | 111 | Substitution | L | M | 1 | 1 |
| Multiple sequence alignment of our canonical and alternatively spliced PANK2 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of PANK2 |
| UniProt-id | ENSG | ENST | ENSP |
| Q9BZ23-1 | ENSG00000125779.24 | ENST00000316562.9 | ENSP00000313377.4 |
| Q9BZ23-2 | ENSG00000125779.24 | ENST00000497424.5 | ENSP00000417609.1 |
| Q9BZ23-2 | ENSG00000125779.24 | ENST00000621507.1 | ENSP00000481523.1 |
| Q9BZ23-4 | ENSG00000125779.24 | ENST00000610179.7 | ENSP00000477429.2 |
| UniProt-id | NM ID | NP ID |
| Q9BZ23-1 | NM_153638.3 | NP_705902.2 |
| Q9BZ23-2 | NM_001324191.1 | NP_001311120.1 |
| Q9BZ23-2 | NM_024960.5 | NP_079236.3 |
| Q9BZ23-2 | NM_153640.3 | NP_705904.1 |
| Amino acid sequences of our canonical and alternatively spliced PANK2 |
| accession_id | Protein sequence |
| Q9BZ23-1 | MRRLGPFHPRVHWAAPPSLSSGLHRLLFLRGTRIPSSTTLSPPRHDSLSLDGGTVNPPRVREPTGREAFGPSPASSDWLPARWRNGRGGR PRARLCSGWTAAEEARRNPTLGGLLGRQRLLLRMGGGRLGAPMERHGRASATSVSSAGEQAAGDPEGRRQEPLRRRASSASVPAVGASAE GTRRDRLGSYSGPTSVSRQRVESLRKKRPLFPWFGLDIGGTLVKLVYFEPKDITAEEEEEEVESLKSIRKYLTSNVAYGSTGIRDVHLEL KDLTLCGRKGNLHFIRFPTHDMPAFIQMGRDKNFSSLHTVFCATGGGAYKFEQDFLTIGDLQLCKLDELDCLIKGILYIDSVGFNGRSQC YYFENPADSEKCQKLPFDLKNPYPLLLVNIGSGVSILAVYSKDNYKRVTGTSLGGGTFFGLCCLLTGCTTFEEALEMASRGDSTKVDKLV RDIYGGDYERFGLPGWAVASSFGNMMSKEKREAVSKEDLARATLITITNNIGSIARMCALNENINQVVFVGNFLRINTIAMRLLAYALDY |
| Q9BZ23-2 | MPAFIQMGRDKNFSSLHTVFCATGGGAYKFEQDFLTIGDLQLCKLDELDCLIKGILYIDSVGFNGRSQCYYFENPADSEKCQKLPFDLKN PYPLLLVNIGSGVSILAVYSKDNYKRVTGTSLGGGTFFGLCCLLTGCTTFEEALEMASRGDSTKVDKLVRDIYGGDYERFGLPGWAVASS FGNMMSKEKREAVSKEDLARATLITITNNIGSIARMCALNENINQVVFVGNFLRINTIAMRLLAYALDYWSKGQLKALFSEHEGYFGAVG |
| Q9BZ23-3 | MGGGRLGAPMERHGRASATSVSSAGEQAAGDPEGRRQEPLRRRASSASVPAVGASAEGTRRDRLGSYSGPTSVSRQRVESLRKKRPLFPW FGLDIGGTLVKLVYFEPKDITAEEEEEEVESLKSIRKYLTSNVAYGSTGIRDVHLELKDLTLCGRKGNLHFIRFPTHDMPAFIQMGRDKN FSSLHTVFCATGGGAYKFEQDFLTIGDLQLCKLDELDCLIKGILYIDSVGFNGRSQCYYFENPADSEKCQKLPFDLKNPYPLLLVNIGSG VSILAVYSKDNYKRVTGTSLGGGTFFGLCCLLTGCTTFEEALEMASRGDSTKVDKLVRDIYGGDYERFGLPGWAVASSFGNMMSKEKREA |
| Q9BZ23-4 | MGGLLGRQRLLLRMGGGRLGAPMERHGRASATSVSSAGEQAAGDPEGRRQEPLRRRASSASVPAVGASAEGTRRDRLGSYSGPTSVSRQR VESLRKKRPLFPWFGLDIGGTLVKLVYFEPKDITAEEEEEEVESLKSIRKYLTSNVAYGSTGIRDVHLELKDLTLCGRKGNLHFIRFPTH DMPAFIQMGRDKNFSSLHTVFCATGGGAYKFEQDFLTIGDLQLCKLDELDCLIKGILYIDSVGFNGRSQCYYFENPADSEKCQKLPFDLK NPYPLLLVNIGSGVSILAVYSKDNYKRVTGTSLGGGTFFGLCCLLTGCTTFEEALEMASRGDSTKVDKLVRDIYGGDYERFGLPGWAVAS SFGNMMSKEKREAVSKEDLARATLITITNNIGSIARMCALNENINQVVFVGNFLRINTIAMRLLAYALDYWSKGQLKALFSEHEGYFGAV |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| PANK2 (go to UniProt):Q9BZ23 |
| 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 |
| Q9BZ23 | Region | 34 | 94 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=291 |
| Q9BZ23 | Region | 34 | 94 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=123 |
| Q9BZ23 | Region | 34 | 94 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=110 |
| Q9BZ23 | Region | 127 | 198 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=291 |
| Q9BZ23 | Motif | 82 | 94 | Note=Nucleolar localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23152917;Dbxref=PMID:23152917 | Type=Deletion;Start=1;End=291 |
| Q9BZ23 | Motif | 82 | 94 | Note=Nucleolar localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23152917;Dbxref=PMID:23152917 | Type=Deletion;Start=1;End=123 |
| Q9BZ23 | Motif | 82 | 94 | Note=Nucleolar localization signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23152917;Dbxref=PMID:23152917 | Type=Deletion;Start=1;End=110 |
| Q9BZ23 | Motif | 268 | 275 | Note=Nuclear export signal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23152917;Dbxref=PMID:23152917 | Type=Deletion;Start=1;End=291 |
Gene Isoform Structures and Expression Levels for PANK2 |
| Gene structures of our canonical and alternative spliced genes of PANK2 * 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 Q9BZ23-1 |
| 3D view using mol* of Q9BZ23-2 |
| 3D view using mol* of Q9BZ23-3 |
| 3D view using mol* of Q9BZ23-4 |
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 Q9BZ23-1 |
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| pLDDT distribution across the protein length of Q9BZ23-2 |
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| pLDDT distribution across the protein length of Q9BZ23-3 |
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| pLDDT distribution across the protein length of Q9BZ23-4 |
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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 Q9BZ23-1 |
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| Ramachandran plot of Q9BZ23-2 |
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| Ramachandran plot of Q9BZ23-3 |
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| Ramachandran plot of Q9BZ23-4 |
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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 |
| Q9BZ23-1 | 1.156 | 85 | 1.232 | 116.62 | 0.414 | 0.839 | 1.13 | 3.419 | 0.424 | 8.058 | 1.153 | 214,216,225,248,251,252,258,259,260,261,262,285,28 7,291,294,295,298,302,304,311 |
| Q9BZ23-2 | 1.041 | 111 | 1.104 | 375.242 | 0.702 | 0.67 | 0.771 | 0.82 | 0.728 | 1.126 | 0.556 | 75,76,152,153,156,158,159,163,172,175,176,177,178, 179,180,200,204,205,208,209,212,238,241,242,245,24 6,250 |
| Q9BZ23-3 | 1.164 | 84 | 1.258 | 119.021 | 0.368 | 0.82 | 1.12 | 3.924 | 0.293 | 13.387 | 0.518 | 91,93,102,125,128,129,135,136,137,138,139,162,164, 168,171,172,175,179,181,188 |
| Q9BZ23-4 | 1.138 | 81 | 1.213 | 122.794 | 0.357 | 0.83 | 1.142 | 3.773 | 0.402 | 9.386 | 0.688 | 104,115,138,141,142,148,149,150,151,152,175,177,18 1,184,185,188,194 |
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 Q9BZ23-1_Q9BZ23-1_5e26_B.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9BZ23-1_5e26_B_Q9BZ23-2.pdb |
| 3D view using mol* of Q9BZ23-1_5e26_B_Q9BZ23-3.pdb |
| 3D view using mol* of Q9BZ23-1_5e26_B_Q9BZ23-4.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of Q9BZ23-1_Q9BZ23-2.pdb |
| 3D view using mol* of Q9BZ23-1_Q9BZ23-3.pdb |
| 3D view using mol* of Q9BZ23-1_Q9BZ23-4.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/Q9BZ23-1_vs_Q9BZ23-2.png |
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| ./stats/secondary_structure/figure/Q9BZ23-1_vs_Q9BZ23-3.png |
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| ./stats/secondary_structure/figure/Q9BZ23-1_vs_Q9BZ23-4.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/Q9BZ23-1_vs_Q9BZ23-2.png |
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| ./stats/relative_asa/Q9BZ23-1_vs_Q9BZ23-3.png |
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| ./stats/relative_asa/Q9BZ23-1_vs_Q9BZ23-4.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 PANK2 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to PANK2 |
| Previous studies relating to the alternative splicing of PANK2 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| PANK2 | 16272150 | Biochemical properties of human pantothenate kinase 2 isoforms and mutations linked to pantothenate kinase-associated neurodegeneration. | The PANK2 gene encodes the human pantothenate kinase 2 protein isoforms, and PANK2 mutations are linked to pantothenate kinase-associated neurodegeneration. Two PanK2 protein forms are proteolytically processed to form a mitochondrially localized, mature PanK2. Another isoform arose from a proposed initiation at a leucine codon and was not processed further. The fifth isoform was postulated to arise from an alternative splicing event and was found to encode an inactive protein. Fourteen mutant PanK2 proteins with single amino acid substitutions, associated with either early or late onset disease, were evaluated for activity. The PanK2(G521R), the most frequent mutation in pantothenate kinase-associated neurodegeneration, was devoid of activity and did not fold properly. However, nine of the mutant proteins associated with disease possessed catalytic activities that were indistinguishable from wild type, including the frequently encountered PanK2(T528M) missense mutation. PanK2 was extremely sensitive to feedback inhibition by CoA thioesters (IC50 values between 250 and 500 nM), and the regulation of the active PanK2 mutants was comparable with that of the wild-type protein. Coexpression of the PanK2(G521R) and wild-type PanK2 did not interfere with wild-type enzyme activity, arguing against a dominant negative effect of the PanK2(G521R) mutation in heterozygous patients. These data described the unique biochemical features of the PanK2 isoforms and suggested that catalytic defects may not be the sole cause for the neurodegenerative phenotype. | D009410 | Nerve Degeneration |
| PANK2 | 16272150 | Biochemical properties of human pantothenate kinase 2 isoforms and mutations linked to pantothenate kinase-associated neurodegeneration. | The PANK2 gene encodes the human pantothenate kinase 2 protein isoforms, and PANK2 mutations are linked to pantothenate kinase-associated neurodegeneration. Two PanK2 protein forms are proteolytically processed to form a mitochondrially localized, mature PanK2. Another isoform arose from a proposed initiation at a leucine codon and was not processed further. The fifth isoform was postulated to arise from an alternative splicing event and was found to encode an inactive protein. Fourteen mutant PanK2 proteins with single amino acid substitutions, associated with either early or late onset disease, were evaluated for activity. The PanK2(G521R), the most frequent mutation in pantothenate kinase-associated neurodegeneration, was devoid of activity and did not fold properly. However, nine of the mutant proteins associated with disease possessed catalytic activities that were indistinguishable from wild type, including the frequently encountered PanK2(T528M) missense mutation. PanK2 was extremely sensitive to feedback inhibition by CoA thioesters (IC50 values between 250 and 500 nM), and the regulation of the active PanK2 mutants was comparable with that of the wild-type protein. Coexpression of the PanK2(G521R) and wild-type PanK2 did not interfere with wild-type enzyme activity, arguing against a dominant negative effect of the PanK2(G521R) mutation in heterozygous patients. These data described the unique biochemical features of the PanK2 isoforms and suggested that catalytic defects may not be the sole cause for the neurodegenerative phenotype. | D006211 | Pantothenate Kinase-Associated Neurodegeneration |
Clinically important variants in PANK2 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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