LOCUS       NP_006205                338 aa            linear   PRI 27-APR-2025
DEFINITION  phytanoyl-CoA dioxygenase, peroxisomal isoform a precursor [Homo
            sapiens].
ACCESSION   NP_006205
VERSION     NP_006205.1
DBSOURCE    REFSEQ: accession NM_006214.4
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  (residues 1 to 338)
  AUTHORS   Daich Varela,M., Schiff,E., Malka,S., Wright,G., Mahroo,O.A.,
            Webster,A.R., Michaelides,M. and Arno,G.
  TITLE     PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is Associated
            With Attenuated Refsum Disease
  JOURNAL   Invest Ophthalmol Vis Sci 65 (2), 38 (2024)
   PUBMED   38411969
  REMARK    GeneRIF: PHYH c.678+5G>T Leads to In-Frame Exon Skipping and Is
            Associated With Attenuated Refsum Disease.
REFERENCE   2  (residues 1 to 338)
  AUTHORS   Zhengqi,Q., Zezhi,G., Lei,J., He,Q., Jinyao,P. and Ying,A.
  TITLE     Prognostic role of PHYH for overall survival (OS) in clear cell
            renal cell carcinoma (ccRCC)
  JOURNAL   Eur J Med Res 26 (1), 9 (2021)
   PUBMED   33468235
  REMARK    GeneRIF: Prognostic role of PHYH for overall survival (OS) in clear
            cell renal cell carcinoma (ccRCC).
            Publication Status: Online-Only
REFERENCE   3  (residues 1 to 338)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   4  (residues 1 to 338)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   5  (residues 1 to 338)
  AUTHORS   Searls,T., Butler,D., Chien,W., Mukherji,M., Lloyd,M.D. and
            Schofield,C.J.
  TITLE     Studies on the specificity of unprocessed and mature forms of
            phytanoyl-CoA 2-hydroxylase and mutation of the iron binding
            ligands
  JOURNAL   J Lipid Res 46 (8), 1660-1667 (2005)
   PUBMED   15930519
  REMARK    GeneRIF: demonstrate that both unprocessed and processed forms are
            able to hydroxylate a range of CoA derivatives; site-directed
            mutagenesis was used to support proposals for the identity of the
            iron binding istes of PAHX
REFERENCE   6  (residues 1 to 338)
  AUTHORS   Jansen,G.A., Wanders,R.J., Watkins,P.A. and Mihalik,S.J.
  TITLE     Phytanoyl-coenzyme A hydroxylase deficiency -- the enzyme defect in
            Refsum's disease
  JOURNAL   N Engl J Med 337 (2), 133-134 (1997)
   PUBMED   9221344
REFERENCE   7  (residues 1 to 338)
  AUTHORS   Jansen,G.A., Mihalik,S.J., Watkins,P.A., Moser,H.W., Jakobs,C.,
            Denis,S. and Wanders,R.J.
  TITLE     Phytanoyl-CoA hydroxylase is present in human liver, located in
            peroxisomes, and deficient in Zellweger syndrome: direct,
            unequivocal evidence for the new, revised pathway of phytanic acid
            alpha-oxidation in humans
  JOURNAL   Biochem Biophys Res Commun 229 (1), 205-210 (1996)
   PUBMED   8954107
REFERENCE   8  (residues 1 to 338)
  AUTHORS   Waterham,H.R., Wanders,R.J.A. and Leroy,B.P.
  TITLE     Adult Refsum Disease
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301527
REFERENCE   9  (residues 1 to 338)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
REFERENCE   10 (residues 1 to 338)
  AUTHORS   Skjeldal,O.H., Stokke,O., Refsum,S., Norseth,J. and Petit,H.
  TITLE     Clinical and biochemical heterogeneity in conditions with phytanic
            acid accumulation
  JOURNAL   J Neurol Sci 77 (1), 87-96 (1987)
   PUBMED   2433405
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC029512.1, AL138764.21 and
            BM351828.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            Summary: This gene is a member of the PhyH family and encodes a
            peroxisomal protein that is involved in the alpha-oxidation of
            3-methyl branched fatty acids. Specifically, this protein converts
            phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Mutations in this gene
            have been associated with Refsum disease (RD) and deficient protein
            activity has been associated with Zellweger syndrome and rhizomelic
            chondrodysplasia punctata. Alternate transcriptional splice
            variants, encoding different isoforms, have been characterized.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) encodes isoform a.
            
            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 :: BC029512.1, SRR3476690.665677.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142586, SAMEA2146411
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000263038.9/ ENSP00000263038.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
FEATURES             Location/Qualifiers
     source          1..338
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10p13"
     Protein         1..338
                     /product="phytanoyl-CoA dioxygenase, peroxisomal isoform a
                     precursor"
                     /EC_number="1.14.11.18"
                     /note="phytanoyl-CoA 2 oxoglutarate dioxygenase; phytanic
                     acid oxidase; phytanoyl-CoA alpha-hydroxylase;
                     phytanoil-CoA alpha hydroxylase; phytanoyl-CoA
                     dioxygenase, peroxisomal"
                     /calculated_mol_wt=35436
     transit_peptide 1..30
                     /note="PTS2 - peroxisomal targeting signal 2"
                     /calculated_mol_wt=3121
     mat_peptide     31..338
                     /product="phytanoyl-CoA dioxygenase, peroxisomal isoform
                     a"
                     /calculated_mol_wt=35436
     Region          61..277
                     /region_name="PhyH"
                     /note="Phytanoyl-CoA dioxygenase (PhyH); pfam05721"
                     /db_xref="CDD:399029"
     Site            317
                     /site_type="phosphorylation"
                     /note="Phosphoserine.
                     /evidence=ECO:0007744|PubMed:24275569; propagated from
                     UniProtKB/Swiss-Prot (O14832.1)"
     CDS             1..338
                     /gene="PHYH"
                     /gene_synonym="LN1; LNAP1; PAHX; PHYH1; RD"
                     /coded_by="NM_006214.4:23..1039"
                     /note="isoform a precursor is encoded by transcript
                     variant 1"
                     /db_xref="CCDS:CCDS7097.1"
                     /db_xref="GeneID:5264"
                     /db_xref="HGNC:HGNC:8940"
                     /db_xref="MIM:602026"
ORIGIN      
        1 meqlraaarl qivlghlgrp sagavvahpt sgtissasfh pqqfqytldn nvltleqrkf
       61 yeengflvik nlvpdadiqr frnefekicr kevkplgltv mrdvtiskse yapsekmitk
      121 vqdfqedkel fryctlpeil kyvecftgpn imamhtmlin kppdsgkkts rhplhqdlhy
      181 fpfrpsdliv cawtamehis rnngclvvlp gthkgslkph dypkweggvn kmfhgiqdye
      241 enkarvhlvm ekgdtvffhp llihgsgqnk tqgfrkaisc hfasadchyi dvkgtsqeni
      301 ekevvgiahk ffgaensvnl kdiwmfrarl vkgertnl
//
