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Protein

Phytanoyl-CoA dioxygenase, peroxisomal

Gene

PHYH

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA.

Catalytic activityi

Phytanoyl-CoA + 2-oxoglutarate + O2 = 2-hydroxyphytanoyl-CoA + succinate + CO2.

Cofactori

Protein has several cofactor binding sites:

Pathwayi: fatty acid metabolism

This protein is involved in the pathway fatty acid metabolism, which is part of Lipid metabolism.
View all proteins of this organism that are known to be involved in the pathway fatty acid metabolism and in Lipid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei120Alpha-ketoglutarate1 Publication1
Binding sitei157Alpha-ketoglutarate1 Publication1
Metal bindingi175Iron1 Publication1
Metal bindingi177Iron1 Publication1
Binding sitei193Alpha-ketoglutarate1 Publication1
Metal bindingi264Iron1 Publication1
Binding sitei266Alpha-ketoglutarate1 Publication1
Binding sitei275Alpha-ketoglutarate1 Publication1

GO - Molecular functioni

  • cofactor binding Source: UniProtKB
  • L-ascorbic acid binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • phytanoyl-CoA dioxygenase activity Source: UniProtKB

GO - Biological processi

  • fatty acid alpha-oxidation Source: UniProtKB
  • isoprenoid metabolic process Source: UniProtKB
  • methyl-branched fatty acid metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Vitamin C

Enzyme and pathway databases

BioCyciMetaCyc:HS03003-MONOMER.
ZFISH:HS03003-MONOMER.
BRENDAi1.14.11.18. 2681.
ReactomeiR-HSA-389599. Alpha-oxidation of phytanate.
UniPathwayiUPA00199.

Chemistry databases

SwissLipidsiSLP:000001017.

Names & Taxonomyi

Protein namesi
Recommended name:
Phytanoyl-CoA dioxygenase, peroxisomal (EC:1.14.11.18)
Alternative name(s):
Phytanic acid oxidase
Phytanoyl-CoA alpha-hydroxylase
Short name:
PhyH
Gene namesi
Name:PHYH
Synonyms:PAHX
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:8940. PHYH.

Subcellular locationi

GO - Cellular componenti

  • mitochondrion Source: Ensembl
  • peroxisomal matrix Source: Reactome
  • peroxisome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Peroxisome

Pathology & Biotechi

Involvement in diseasei

Refsum disease (RD)4 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare autosomal recessive peroxisomal disorder characterized by the accumulation of the branched-chain fatty acid, phytanic acid, in blood and tissues. Cardinal clinical features are retinitis pigmentosa, peripheral neuropathy, cerebellar ataxia, and elevated protein levels in the cerebrospinal fluid (CSF). Half of all patients exhibit generalized, mild to moderate ichthyosis resembling ichthyosis vulgaris. Less constant features are nerve deafness, anosmia, skeletal abnormalities, cataracts and cardiac impairment.
See also OMIM:266500
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01748229P → S in RD; unknown pathological significance. 1 PublicationCorresponds to variant rs28938169dbSNPEnsembl.1
Natural variantiVAR_01861983N → Y in RD. 1
Natural variantiVAR_017483173P → S in RD. 1 Publication1
Natural variantiVAR_018631175H → R in RD. 1
Natural variantiVAR_017484176Q → K in RD. 1 PublicationCorresponds to variant rs28939672dbSNPEnsembl.1
Natural variantiVAR_017485177D → G in RD; total loss of activity. 1 PublicationCorresponds to variant rs770262329dbSNPEnsembl.1
Natural variantiVAR_012980192A → AA in RD. 1 Publication1
Natural variantiVAR_017486193W → R in RD. 1 Publication1
Natural variantiVAR_017487197E → Q in RD. 1 Publication1
Natural variantiVAR_017488199I → F in RD. 1 Publication1
Natural variantiVAR_017489204G → S in RD; total loss of activity. 2 PublicationsCorresponds to variant rs28939673dbSNPEnsembl.1
Natural variantiVAR_017490220H → Y in RD. 1 PublicationCorresponds to variant rs767216891dbSNPEnsembl.1
Natural variantiVAR_017492257F → S in RD. 1 Publication1
Natural variantiVAR_005525269N → H in RD. 2 PublicationsCorresponds to variant rs104894179dbSNPEnsembl.1
Natural variantiVAR_017493275R → Q in RD; total loss of activity. 1 PublicationCorresponds to variant rs28939674dbSNPEnsembl.1
Natural variantiVAR_005526275R → W in RD; total loss of activity. 2 PublicationsCorresponds to variant rs28939671dbSNPEnsembl.1

Keywords - Diseasei

Cataract, Deafness, Disease mutation, Ichthyosis, Peroxisome biogenesis disorder, Retinitis pigmentosa

Organism-specific databases

DisGeNETi5264.
MalaCardsiPHYH.
MIMi266500. phenotype.
OpenTargetsiENSG00000107537.
Orphaneti773. Refsum disease.
PharmGKBiPA33280.

Chemistry databases

DrugBankiDB00025. Antihemophilic Factor (Recombinant).
DB00126. Vitamin C.

Polymorphism and mutation databases

BioMutaiPHYH.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 30PeroxisomeBy similarityAdd BLAST30
ChainiPRO_000002405331 – 338Phytanoyl-CoA dioxygenase, peroxisomalAdd BLAST308

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei59N6-succinyllysineBy similarity1
Modified residuei108N6-succinyllysineBy similarity1
Modified residuei231N6-succinyllysineBy similarity1
Modified residuei252N6-succinyllysineBy similarity1
Modified residuei317PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO14832.
PaxDbiO14832.
PeptideAtlasiO14832.
PRIDEiO14832.

PTM databases

iPTMnetiO14832.
PhosphoSitePlusiO14832.

Expressioni

Tissue specificityi

Expressed in liver, kidney, and T-cells, but not in spleen, brain, heart, lung and skeletal muscle.

Gene expression databases

BgeeiENSG00000107537.
CleanExiHS_PHYH.
ExpressionAtlasiO14832. baseline and differential.
GenevisibleiO14832. HS.

Organism-specific databases

HPAiHPA007598.
HPA011796.

Interactioni

Subunit structurei

Interacts specifically with the immunophilin FKBP52 and PHYHIP.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
FAM9BQ8IZU03EBI-721853,EBI-10175124

Protein-protein interaction databases

BioGridi111282. 12 interactors.
IntActiO14832. 6 interactors.
MINTiMINT-1411634.
STRINGi9606.ENSP00000263038.

Structurei

Secondary structure

1338
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi57 – 64Combined sources8
Beta strandi65 – 69Combined sources5
Helixi75 – 89Combined sources15
Beta strandi99 – 101Combined sources3
Beta strandi104 – 106Combined sources3
Beta strandi115 – 117Combined sources3
Beta strandi120 – 122Combined sources3
Helixi128 – 135Combined sources8
Helixi137 – 147Combined sources11
Beta strandi149 – 161Combined sources13
Helixi177 – 180Combined sources4
Helixi186 – 188Combined sources3
Beta strandi189 – 197Combined sources9
Beta strandi206 – 208Combined sources3
Helixi212 – 214Combined sources3
Beta strandi246 – 248Combined sources3
Beta strandi255 – 258Combined sources4
Beta strandi264 – 266Combined sources3
Beta strandi271 – 273Combined sources3
Beta strandi275 – 284Combined sources10
Helixi296 – 301Combined sources6
Helixi320 – 327Combined sources8
Beta strandi329 – 333Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2A1XX-ray2.50A31-338[»]
DisProtiDP00327.
ProteinModelPortaliO14832.
SMRiO14832.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO14832.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni175 – 177Alpha-ketoglutarate binding3

Sequence similaritiesi

Belongs to the PhyH family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IPBI. Eukaryota.
COG5285. LUCA.
GeneTreeiENSGT00390000001775.
HOGENOMiHOG000007341.
HOVERGENiHBG000392.
InParanoidiO14832.
KOiK00477.
OMAiWTAMERV.
OrthoDBiEOG091G0F66.
PhylomeDBiO14832.
TreeFamiTF313667.

Family and domain databases

InterProiIPR008775. Phytyl_CoA_dOase.
[Graphical view]
PfamiPF05721. PhyH. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O14832-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEQLRAAARL QIVLGHLGRP SAGAVVAHPT SGTISSASFH PQQFQYTLDN
60 70 80 90 100
NVLTLEQRKF YEENGFLVIK NLVPDADIQR FRNEFEKICR KEVKPLGLTV
110 120 130 140 150
MRDVTISKSE YAPSEKMITK VQDFQEDKEL FRYCTLPEIL KYVECFTGPN
160 170 180 190 200
IMAMHTMLIN KPPDSGKKTS RHPLHQDLHY FPFRPSDLIV CAWTAMEHIS
210 220 230 240 250
RNNGCLVVLP GTHKGSLKPH DYPKWEGGVN KMFHGIQDYE ENKARVHLVM
260 270 280 290 300
EKGDTVFFHP LLIHGSGQNK TQGFRKAISC HFASADCHYI DVKGTSQENI
310 320 330
EKEVVGIAHK FFGAENSVNL KDIWMFRARL VKGERTNL
Length:338
Mass (Da):38,538
Last modified:January 1, 1998 - v1
Checksum:iFBF9639E7C79A6B0
GO
Isoform 2 (identifier: O14832-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-100: Missing.

Note: No experimental confirmation available. Gene prediction based on EST data.
Show »
Length:238
Mass (Da):27,291
Checksum:iBB9006A60F16E0C6
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01748229P → S in RD; unknown pathological significance. 1 PublicationCorresponds to variant rs28938169dbSNPEnsembl.1
Natural variantiVAR_01861983N → Y in RD. 1
Natural variantiVAR_017483173P → S in RD. 1 Publication1
Natural variantiVAR_018631175H → R in RD. 1
Natural variantiVAR_017484176Q → K in RD. 1 PublicationCorresponds to variant rs28939672dbSNPEnsembl.1
Natural variantiVAR_017485177D → G in RD; total loss of activity. 1 PublicationCorresponds to variant rs770262329dbSNPEnsembl.1
Natural variantiVAR_012980192A → AA in RD. 1 Publication1
Natural variantiVAR_017486193W → R in RD. 1 Publication1
Natural variantiVAR_017487197E → Q in RD. 1 Publication1
Natural variantiVAR_017488199I → F in RD. 1 Publication1
Natural variantiVAR_017489204G → S in RD; total loss of activity. 2 PublicationsCorresponds to variant rs28939673dbSNPEnsembl.1
Natural variantiVAR_050528215G → S.Corresponds to variant rs7901902dbSNPEnsembl.1
Natural variantiVAR_017490220H → Y in RD. 1 PublicationCorresponds to variant rs767216891dbSNPEnsembl.1
Natural variantiVAR_017491245R → Q.2 PublicationsCorresponds to variant rs62619919dbSNPEnsembl.1
Natural variantiVAR_017492257F → S in RD. 1 Publication1
Natural variantiVAR_005525269N → H in RD. 2 PublicationsCorresponds to variant rs104894179dbSNPEnsembl.1
Natural variantiVAR_017493275R → Q in RD; total loss of activity. 1 PublicationCorresponds to variant rs28939674dbSNPEnsembl.1
Natural variantiVAR_005526275R → W in RD; total loss of activity. 2 PublicationsCorresponds to variant rs28939671dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0462891 – 100Missing in isoform 2. CuratedAdd BLAST100

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF023462 mRNA. Translation: AAB81834.1.
AF112977 mRNA. Translation: AAD20602.1.
AF242386
, AF242379, AF242380, AF242381, AF242382, AF242383, AF242384, AF242385 Genomic DNA. Translation: AAF74123.1.
AL138764 Genomic DNA. Translation: CAI12911.2.
BC029512 mRNA. Translation: AAH29512.1.
CCDSiCCDS41489.1. [O14832-2]
CCDS7097.1. [O14832-1]
RefSeqiNP_001032626.1. NM_001037537.1. [O14832-2]
NP_001310009.1. NM_001323080.1. [O14832-2]
NP_006205.1. NM_006214.3. [O14832-1]
UniGeneiHs.498732.

Genome annotation databases

EnsembliENST00000263038; ENSP00000263038; ENSG00000107537. [O14832-1]
ENST00000396913; ENSP00000380121; ENSG00000107537. [O14832-2]
GeneIDi5264.
KEGGihsa:5264.
UCSCiuc001ime.4. human. [O14832-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF023462 mRNA. Translation: AAB81834.1.
AF112977 mRNA. Translation: AAD20602.1.
AF242386
, AF242379, AF242380, AF242381, AF242382, AF242383, AF242384, AF242385 Genomic DNA. Translation: AAF74123.1.
AL138764 Genomic DNA. Translation: CAI12911.2.
BC029512 mRNA. Translation: AAH29512.1.
CCDSiCCDS41489.1. [O14832-2]
CCDS7097.1. [O14832-1]
RefSeqiNP_001032626.1. NM_001037537.1. [O14832-2]
NP_001310009.1. NM_001323080.1. [O14832-2]
NP_006205.1. NM_006214.3. [O14832-1]
UniGeneiHs.498732.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2A1XX-ray2.50A31-338[»]
DisProtiDP00327.
ProteinModelPortaliO14832.
SMRiO14832.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111282. 12 interactors.
IntActiO14832. 6 interactors.
MINTiMINT-1411634.
STRINGi9606.ENSP00000263038.

Chemistry databases

DrugBankiDB00025. Antihemophilic Factor (Recombinant).
DB00126. Vitamin C.
SwissLipidsiSLP:000001017.

PTM databases

iPTMnetiO14832.
PhosphoSitePlusiO14832.

Polymorphism and mutation databases

BioMutaiPHYH.

Proteomic databases

MaxQBiO14832.
PaxDbiO14832.
PeptideAtlasiO14832.
PRIDEiO14832.

Protocols and materials databases

DNASUi5264.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263038; ENSP00000263038; ENSG00000107537. [O14832-1]
ENST00000396913; ENSP00000380121; ENSG00000107537. [O14832-2]
GeneIDi5264.
KEGGihsa:5264.
UCSCiuc001ime.4. human. [O14832-1]

Organism-specific databases

CTDi5264.
DisGeNETi5264.
GeneCardsiPHYH.
GeneReviewsiPHYH.
HGNCiHGNC:8940. PHYH.
HPAiHPA007598.
HPA011796.
MalaCardsiPHYH.
MIMi266500. phenotype.
602026. gene.
neXtProtiNX_O14832.
OpenTargetsiENSG00000107537.
Orphaneti773. Refsum disease.
PharmGKBiPA33280.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IPBI. Eukaryota.
COG5285. LUCA.
GeneTreeiENSGT00390000001775.
HOGENOMiHOG000007341.
HOVERGENiHBG000392.
InParanoidiO14832.
KOiK00477.
OMAiWTAMERV.
OrthoDBiEOG091G0F66.
PhylomeDBiO14832.
TreeFamiTF313667.

Enzyme and pathway databases

UniPathwayiUPA00199.
BioCyciMetaCyc:HS03003-MONOMER.
ZFISH:HS03003-MONOMER.
BRENDAi1.14.11.18. 2681.
ReactomeiR-HSA-389599. Alpha-oxidation of phytanate.

Miscellaneous databases

EvolutionaryTraceiO14832.
GenomeRNAii5264.
PROiO14832.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000107537.
CleanExiHS_PHYH.
ExpressionAtlasiO14832. baseline and differential.
GenevisibleiO14832. HS.

Family and domain databases

InterProiIPR008775. Phytyl_CoA_dOase.
[Graphical view]
PfamiPF05721. PhyH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPAHX_HUMAN
AccessioniPrimary (citable) accession number: O14832
Secondary accession number(s): A8MTS8, B1ALH5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: January 1, 1998
Last modified: November 30, 2016
This is version 168 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.