LOCUS       NM_018129               3417 bp    mRNA    linear   PRI 24-FEB-2025
DEFINITION  Homo sapiens pyridoxamine 5'-phosphate oxidase (PNPO), transcript
            variant 1, mRNA.
ACCESSION   NM_018129
VERSION     NM_018129.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3417)
  AUTHORS   Clark,N.E., Katolik,A., Gallant,P., Welch,A., Murphy,E., Buerer,L.,
            Schorl,C., Naik,N., Naik,M.T., Holloway,S.P., Cano,K.,
            Weintraub,S.T., Howard,K.M., Hart,P.J., Jogl,G., Damha,M.J. and
            Fairbrother,W.G.
  TITLE     Activation of human RNA lariat debranching enzyme Dbr1 by binding
            protein TTDN1 occurs though an intrinsically disordered C-terminal
            domain
  JOURNAL   J Biol Chem 299 (9), 105100 (2023)
   PUBMED   37507019
  REMARK    GeneRIF: Activation of human RNA lariat debranching enzyme Dbr1 by
            binding protein TTDN1 occurs though an intrinsically disordered
            C-terminal domain.
REFERENCE   2  (bases 1 to 3417)
  AUTHORS   Morgenstern,M., Peikert,C.D., Lubbert,P., Suppanz,I., Klemm,C.,
            Alka,O., Steiert,C., Naumenko,N., Schendzielorz,A., Melchionda,L.,
            Muhlhauser,W.W.D., Knapp,B., Busch,J.D., Stiller,S.B.,
            Dannenmaier,S., Lindau,C., Licheva,M., Eickhorst,C., Galbusera,R.,
            Zerbes,R.M., Ryan,M.T., Kraft,C., Kozjak-Pavlovic,V., Drepper,F.,
            Dennerlein,S., Oeljeklaus,S., Pfanner,N., Wiedemann,N. and
            Warscheid,B.
  TITLE     Quantitative high-confidence human mitochondrial proteome and its
            dynamics in cellular context
  JOURNAL   Cell Metab 33 (12), 2464-2483 (2021)
   PUBMED   34800366
REFERENCE   3  (bases 1 to 3417)
  AUTHORS   Barile,A., Mills,P., di Salvo,M.L., Graziani,C., Bunik,V.,
            Clayton,P., Contestabile,R. and Tramonti,A.
  TITLE     Characterization of Novel Pathogenic Variants Causing
            Pyridox(am)ine 5'-Phosphate Oxidase-Dependent Epilepsy
  JOURNAL   Int J Mol Sci 22 (21), 12013 (2021)
   PUBMED   34769443
  REMARK    GeneRIF: Characterization of Novel Pathogenic Variants Causing
            Pyridox(am)ine 5'-Phosphate Oxidase-Dependent Epilepsy.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3417)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   5  (bases 1 to 3417)
  AUTHORS   Alghamdi,M., Bashiri,F.A., Abdelhakim,M., Adly,N., Jamjoom,D.Z.,
            Sumaily,K.M., Alghanem,B. and Arold,S.T.
  TITLE     Phenotypic and molecular spectrum of pyridoxamine-5'-phosphate
            oxidase deficiency: A scoping review of 87 cases of
            pyridoxamine-5'-phosphate oxidase deficiency
  JOURNAL   Clin Genet 99 (1), 99-110 (2021)
   PUBMED   32888189
  REMARK    GeneRIF: Phenotypic and molecular spectrum of
            pyridoxamine-5'-phosphate oxidase deficiency: A scoping review of
            87 cases of pyridoxamine-5'-phosphate oxidase deficiency.
REFERENCE   6  (bases 1 to 3417)
  AUTHORS   Kang,J.H., Hong,M.L., Kim,D.W., Park,J., Kang,T.C., Won,M.H.,
            Baek,N.I., Moon,B.J., Choi,S.Y. and Kwon,O.S.
  TITLE     Genomic organization, tissue distribution and deletion mutation of
            human pyridoxine 5'-phosphate oxidase
  JOURNAL   Eur J Biochem 271 (12), 2452-2461 (2004)
   PUBMED   15182361
  REMARK    GeneRIF: Results describe a combined computer and biochemical
            approach to characterize human pyridoxine 5'-phosphate oxidase
            (PNPO).
REFERENCE   7  (bases 1 to 3417)
  AUTHORS   Musayev,F.N., Di Salvo,M.L., Ko,T.P., Schirch,V. and Safo,M.K.
  TITLE     Structure and properties of recombinant human pyridoxine
            5'-phosphate oxidase
  JOURNAL   Protein Sci 12 (7), 1455-1463 (2003)
   PUBMED   12824491
REFERENCE   8  (bases 1 to 3417)
  AUTHORS   McCormick,D.B. and Chen,H.
  TITLE     Update on interconversions of vitamin B-6 with its coenzyme
  JOURNAL   J Nutr 129 (2), 325-327 (1999)
   PUBMED   10024608
  REMARK    Review article
REFERENCE   9  (bases 1 to 3417)
  AUTHORS   Ngo,E.O., LePage,G.R., Thanassi,J.W., Meisler,N. and Nutter,L.M.
  TITLE     Absence of pyridoxine-5'-phosphate oxidase (PNPO) activity in
            neoplastic cells: isolation, characterization, and expression of
            PNPO cDNA
  JOURNAL   Biochemistry 37 (21), 7741-7748 (1998)
   PUBMED   9601034
REFERENCE   10 (bases 1 to 3417)
  AUTHORS   Plecko,B. and Mills,P.
  TITLE     PNPO Deficiency
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   35737815
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK001397.1, BC006525.2,
            AC018521.8 and CB853441.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_018129.3.
            
            Summary: The enzyme encoded by this gene catalyzes the terminal,
            rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also
            known as vitamin B6. Vitamin B6 is a required co-factor for enzymes
            involved in both homocysteine metabolism and synthesis of
            neurotransmitters such as catecholamine. Mutations in this gene
            result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a
            form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct
            2008].
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK001397.1, SRR7346977.1085016.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000642017.2/ ENSP00000493302.2
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1070              AK001397.1         1-1070
            1071-1548           BC006525.2         1006-1483
            1549-2899           AC018521.8         48428-49778         c
            2900-3417           CB853441.1         18-535              c
FEATURES             Location/Qualifiers
     source          1..3417
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17q21.32"
     gene            1..3417
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /note="pyridoxamine 5'-phosphate oxidase"
                     /db_xref="GeneID:55163"
                     /db_xref="HGNC:HGNC:30260"
                     /db_xref="MIM:603287"
     exon            1..243
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     CDS             106..891
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /EC_number="1.4.3.5"
                     /note="isoform 1 is encoded by transcript variant 1;
                     pyridoxine 5'-phosphate oxidase; pyridoxal 5'-phosphate
                     synthase; pyridoxamine-phosphate oxidase; epididymis
                     secretory protein Li 302; epididymis secretory sperm
                     binding protein"
                     /codon_start=1
                     /product="pyridoxine-5'-phosphate oxidase isoform 1"
                     /protein_id="NP_060599.1"
                     /db_xref="CCDS:CCDS11522.1"
                     /db_xref="GeneID:55163"
                     /db_xref="HGNC:HGNC:30260"
                     /db_xref="MIM:603287"
                     /translation="MTCWLRGVTATFGRPAEWPGYLSHLCGRSAAMDLGPMRKSYRGD
                     REAFEETHLTSLDPVKQFAAWFEEAVQCPDIGEANAMCLATCTRDGKPSARMLLLKGF
                     GKDGFRFFTNFESRKGKELDSNPFASLVFYWEPLNRQVRVEGPVKKLPEEEAECYFHS
                     RPKSSQIGAVVSHQSSVIPDREYLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEF
                     WQGQTNRLHDRIVFRRGLPTGDSPLGPMTHRGEEDWLYERLAP"
     exon            244..368
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     exon            369..468
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     exon            469..522
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     exon            523..651
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     exon            652..722
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     exon            723..3417
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2364..2369
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /note="hexamer: ATTAAA"
     polyA_site      2398
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
     regulatory      3390..3395
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /note="hexamer: AATAAA"
     polyA_site      3417
                     /gene="PNPO"
                     /gene_synonym="HEL-S-302; PDXPO"
                     /note="major polyA site"
ORIGIN      
        1 aaatccttcc ttccccgggg tagaagtcca gggtgagaaa ttggttccga actcaaagga
       61 acccagtgcc gggccacagc cgggtcacgt ggccggcggc cccccatgac gtgctggctg
      121 cggggcgtca cggcgacgtt cgggcgacct gccgagtggc caggctacct cagtcacctg
      181 tgtggtcgca gtgctgccat ggacctggga cccatgcgca agagttaccg cggggaccga
      241 gaggcatttg aggagactca tctgacctcc cttgacccag tgaaacagtt tgctgcctgg
      301 tttgaggagg ctgttcagtg tcctgacata ggggaagcca atgccatgtg tctggctacc
      361 tgcaccagag atggaaaacc ctctgctcgc atgttgctgc tgaagggctt cgggaaagat
      421 ggcttccgct tcttcactaa cttcgagagt cgaaaaggaa aagagctgga ctctaatccc
      481 tttgcttccc ttgtcttcta ctgggagcca cttaaccgtc aggtgcgtgt ggaaggccct
      541 gtgaagaaac tgcctgagga ggaggctgag tgctacttcc actcccgccc caagagcagc
      601 cagattgggg ctgtggtcag ccaccagagt tctgtgatcc ctgatcggga gtatctgaga
      661 aagaaaaatg aggaactgga acagctctac caggatcaag aggtgcccaa gccaaaatcc
      721 tggggtggct atgtcctgta ccctcaggtg atggagttct ggcaaggtca aaccaaccgc
      781 ctgcatgacc ggatagtctt tcggcggggc ctacccacag gagattcccc tttggggccc
      841 atgacccacc gcggggagga agactggctc tatgagagac ttgcacctta actctgggac
      901 ctgctggccc agagtggagc tagggctagg tgtcaagaga gggtgtggga ttgggaccca
      961 ggcccttctt tctaaactca acccatttcc ctccctaccc cttatcttca ggactcttca
     1021 gagctaatcc tctaagttct ctgtactcag ttggttctca gttagctggt caagtggagt
     1081 gtaatggtgg cgtagagaat cacaaatgga aaataattcc ataattattt ttttgacctt
     1141 gcctatgatt gattaggata gctccctcta ggggtagcag ccggtgtgac tccctttctg
     1201 gtgacagaca gggccccagc agccctgtct gttaccatgt gagtcatact ggccaaagct
     1261 tagtcctagc atatgcacct gagccaacct ggccaatcag attgttttgt caataatttg
     1321 aaatttgaac tggagagatc cagaaccttg ggagtcatta aagccaagtc attcatagca
     1381 gccaggaaac aataggaacc aaaagcctct gcctgctgct attgcaattc ccaggatctc
     1441 tccttccctg gatccctccc tcccaggtct gggctgtgca gttcctcccc ctgccttaaa
     1501 acaccccact atctctgtaa agtctctctc tctctttttt ttttttttac ttaatctagc
     1561 tagaatctat ttctgttgat tacaacttaa ctaactcatt tacggatagg actttttttt
     1621 ttcttttttt cttttttctt ttcttttttt tttttgagat ggagtctcac tctgtcaccc
     1681 aggctggagt gcagtggtgt gatcttggct cactgcaacc tctgcctccc aggttcaagc
     1741 aattctcctg cctcagcctc ccaagtagct gggactacag gcacacgcca ccacacccaa
     1801 ctaatttttg tatttttagt agagatgggg tttcaccatg ttggccagga ttgtctccat
     1861 ctcttgacct tgtgatccac ccacctcagc ctcccaaagt gctgggatta caggcatgag
     1921 ccaccacacc cagcgagacg gggtttcatt atgttggcca ggctggtctc caactcctga
     1981 cctaaagtga tctgcccgcc ttggcctccc aaagtgctgg gattacagac atgagccacc
     2041 acgcttggcc gggatagtat atttttatag cacttcccct actgattgct gccttctctg
     2101 tggctacaag ggacccacag aattacaggg aagttacagg gaagcaggtt tcatctcaat
     2161 attgggagag atttcaaaca atcacacctg cctgagaagg agtgggctgt cactaggaat
     2221 ttttattccc agtccgtcag gaattttgta gaagggcttc atgtgctggt accaatagga
     2281 caggaagatt ttaatcagct ttactatcta tgttttttta tggaaactgt gtgtatgtat
     2341 acatacattt tccaaaaaga aaaattaaat gattatagag attatgtttt tcagactact
     2401 cacgtatctg cttttcttac tccccacctc tgctgataat tcctagttca ttggtttttc
     2461 ccccacactg gaattacctg gggagcttaa aaaaccctga tgcctgggtc ccaccctcag
     2521 agatgattga accagcctgg ccagcatggc aaaaccctgt ctctactatg atatgaatgc
     2581 agcctgggca ctgggaaatt taaaaactcc ccagataatt ctgtgcagcc aaggttgaga
     2641 cctcctagtc tagagctttg ctatacacag ggtggtccac aagccaggag catcagcatc
     2701 acttggcagc gccttagaga ttcagacccc agacccactg aatctgaccc tgcattttca
     2761 ctagacccca ggtgatcagc tgcactagac tcaacctcta aaccaagacc tcccaccctc
     2821 acagtctatg atcctttagt gaccctcagc tgagtcctgt gctgaactgt gtttgttctc
     2881 cttgagcaca tgcccgctaa ccagggacag actggatgag caagcaacct gctggctatg
     2941 gagaagagcc aggctgggta aatgtttgct gtgactaagc caggatcaaa gaactgcctg
     3001 ttgcttgcac tggctggcac tgagcttgcc actctgtgaa ctgtgcttcc ttcccctgca
     3061 tggacctgtg cctcagtcac tattatccgc aggccttctc caagggcagc cctctccttg
     3121 tttatccctc ttaagcctgc gtgcaggaag gcacattaac cctgtggccc cctgcaggca
     3181 ggagggtgtt gggtgccctt acctaccttg ccctttttct tgtaccgtag gctgtgccgt
     3241 ttatgagtaa gtgatgtgtg tctgtgtgtg tgtctagaag tgctgcactc accttgtgtt
     3301 attggaggtt gtgtaacccc ctagctttga gcctggtctc agatgttcct tttccgttct
     3361 ctgtccagcc gttaccgccc ccagtctgta ataaaagcct atcagccgtg cacttta
//
