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Protein

Phytanoyl-CoA dioxygenase domain-containing protein 1

Gene

PHYHD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Isoform 1 has alpha-ketoglutarate-dependent dioxygenase activity. Does not show detectable activity towards fatty acid CoA thioesters. Is not expected to be active with phytanoyl CoA. Isoform 2 and isoform 3 probably lack enzyme activity.1 Publication

Cofactori

Fe cation1 Publication

Enzyme regulationi

Activity is increased by ascorbate. Inhibited by myristoyl-CoA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei102Alpha-ketoglutarateBy similarity1
Binding sitei141Alpha-ketoglutarateBy similarity1
Metal bindingi156IronBy similarity1
Metal bindingi158IronBy similarity1
Binding sitei174Alpha-ketoglutarateBy similarity1
Metal bindingi246IronBy similarity1
Binding sitei248Alpha-ketoglutarateBy similarity1
Binding sitei257Alpha-ketoglutarateBy similarity1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Phytanoyl-CoA dioxygenase domain-containing protein 1 (EC:1.-.-.-)
Gene namesi
Name:PHYHD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:23396. PHYHD1.

Pathology & Biotechi

Organism-specific databases

DisGeNETi254295.
OpenTargetsiENSG00000175287.
PharmGKBiPA134959674.

Polymorphism and mutation databases

BioMutaiPHYHD1.
DMDMi166220781.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003136331 – 291Phytanoyl-CoA dioxygenase domain-containing protein 1Add BLAST291

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei55PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ5SRE7.
MaxQBiQ5SRE7.
PaxDbiQ5SRE7.
PeptideAtlasiQ5SRE7.
PRIDEiQ5SRE7.

PTM databases

iPTMnetiQ5SRE7.
PhosphoSitePlusiQ5SRE7.

Expressioni

Gene expression databases

BgeeiENSG00000175287.
CleanExiHS_PHYHD1.
ExpressionAtlasiQ5SRE7. baseline and differential.
GenevisibleiQ5SRE7. HS.

Organism-specific databases

HPAiHPA012115.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
POT1Q9NUX52EBI-2623130,EBI-752420

Protein-protein interaction databases

BioGridi129029. 3 interactors.
IntActiQ5SRE7. 2 interactors.
MINTiMINT-6768910.
STRINGi9606.ENSP00000309515.

Structurei

Secondary structure

1291
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 15Combined sources10
Beta strandi16 – 20Combined sources5
Helixi26 – 41Combined sources16
Helixi47 – 49Combined sources3
Helixi56 – 71Combined sources16
Turni72 – 75Combined sources4
Beta strandi76 – 81Combined sources6
Helixi83 – 85Combined sources3
Beta strandi88 – 90Combined sources3
Beta strandi92 – 94Combined sources3
Helixi96 – 98Combined sources3
Beta strandi99 – 105Combined sources7
Helixi107 – 110Combined sources4
Helixi112 – 118Combined sources7
Helixi121 – 130Combined sources10
Beta strandi133 – 143Combined sources11
Turni147 – 149Combined sources3
Beta strandi153 – 156Combined sources4
Helixi158 – 160Combined sources3
Beta strandi164 – 168Combined sources5
Beta strandi170 – 178Combined sources9
Turni182 – 185Combined sources4
Beta strandi187 – 190Combined sources4
Beta strandi194 – 196Combined sources3
Beta strandi199 – 204Combined sources6
Beta strandi207 – 209Combined sources3
Beta strandi213 – 217Combined sources5
Helixi224 – 226Combined sources3
Beta strandi228 – 230Combined sources3
Beta strandi237 – 241Combined sources5
Beta strandi245 – 248Combined sources4
Beta strandi253 – 255Combined sources3
Beta strandi259 – 266Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OPWX-ray1.90A1-291[»]
3OBZX-ray2.15A1-291[»]
ProteinModelPortaliQ5SRE7.
SMRiQ5SRE7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SRE7.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni156 – 158Alpha-ketoglutarate bindingBy similarity3

Sequence similaritiesi

Belongs to the PhyH family. PHYHD1 subfamily.Curated

Phylogenomic databases

eggNOGiKOG3290. Eukaryota.
ENOG410XUSH. LUCA.
GeneTreeiENSGT00390000006287.
HOVERGENiHBG054973.
InParanoidiQ5SRE7.
OMAiSSTEKWC.
PhylomeDBiQ5SRE7.
TreeFamiTF300011.

Family and domain databases

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

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5SRE7-1) [UniParc]FASTAAdd to basket
Also known as: A, PHYHD1A

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
MACLSPSQLQ KFQQDGFLVL EGFLSAEECV AMQQRIGEIV AEMDVPLHCR
60 70 80 90 100
TEFSTQEEEQ LRAQGSTDYF LSSGDKIRFF FEKGVFDEKG NFLVPPEKSI
110 120 130 140 150
NKIGHALHAH DPVFKSITHS FKVQTLARSL GLQMPVVVQS MYIFKQPHFG
160 170 180 190 200
GEVSPHQDAS FLYTEPLGRV LGVWIAVEDA TLENGCLWFI PGSHTSGVSR
210 220 230 240 250
RMVRAPVGSA PGTSFLGSEP ARDNSLFVPT PVQRGALVLI HGEVVHKSKQ
260 270 280 290
NLSDRSRQAY TFHLMEASGT TWSPENWLQP TAELPFPQLY T
Length:291
Mass (Da):32,411
Last modified:January 15, 2008 - v2
Checksum:i7796A6C35A2E97DD
GO
Isoform 2 (identifier: Q5SRE7-2) [UniParc]FASTAAdd to basket
Also known as: C, PHYHD1C

The sequence of this isoform differs from the canonical sequence as follows:
     125-145: Missing.

Show »
Length:270
Mass (Da):30,047
Checksum:iF28E4D75E929904E
GO
Isoform 3 (identifier: Q5SRE7-3) [UniParc]FASTAAdd to basket
Also known as: B, PHYHD1B

The sequence of this isoform differs from the canonical sequence as follows:
     146-291: QPHFGGEVSP...AELPFPQLYT → SPLIRTPPSC...RRAGALAPPG

Show »
Length:297
Mass (Da):32,668
Checksum:i806C69D3A9D997A0
GO

Sequence cautioni

The sequence CAI10840 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAO72146 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAO72147 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Isoform 3 (identifier: Q5SRE7-3)
Sequence conflicti193E → G in AAH09373 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_050529222R → W.Corresponds to variant rs10988159dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_030077125 – 145Missing in isoform 2. 1 PublicationAdd BLAST21
Alternative sequenceiVSP_030078146 – 291QPHFG…PQLYT → SPLIRTPPSCTRSPWAGCWA CGSQWRMPRWRTAVSGSSLA PTPVVCQEGWSGPLLAQRLV PASLGQSQPGITASLCPPQC REGPWSSSMEKWYTRASRTS LTARARPTLSTSWRPLAPPG ARRTGSSQQLNCPFPNCTPK GSRRAGALAPPG in isoform 3. 1 PublicationAdd BLAST146

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK095000 mRNA. Translation: BAG52969.1.
AL672142 Genomic DNA. Translation: CAI10840.1. Sequence problems.
AL672142 Genomic DNA. Translation: CAI10842.1.
AL672142 Genomic DNA. Translation: CAI10843.1.
AL672142 Genomic DNA. Translation: CAO72146.1. Sequence problems.
AL672142 Genomic DNA. Translation: CAO72147.1. Sequence problems.
AL672142 Genomic DNA. Translation: CAQ77683.1.
CH471090 Genomic DNA. Translation: EAW87844.1.
CH471090 Genomic DNA. Translation: EAW87845.1.
CH471090 Genomic DNA. Translation: EAW87847.1.
BC009373 mRNA. Translation: AAH09373.1.
BC051300 mRNA. Translation: AAH51300.1.
BC053853 mRNA. Translation: AAH53853.1.
CCDSiCCDS43885.1. [Q5SRE7-1]
CCDS43886.1. [Q5SRE7-2]
CCDS6914.1. [Q5SRE7-3]
RefSeqiNP_001094346.1. NM_001100876.1. [Q5SRE7-1]
NP_001094347.1. NM_001100877.1. [Q5SRE7-2]
NP_777593.2. NM_174933.3. [Q5SRE7-3]
UniGeneiHs.709447.

Genome annotation databases

EnsembliENST00000308941; ENSP00000309515; ENSG00000175287. [Q5SRE7-3]
ENST00000353176; ENSP00000340945; ENSG00000175287. [Q5SRE7-2]
ENST00000372592; ENSP00000361673; ENSG00000175287. [Q5SRE7-1]
ENST00000421063; ENSP00000409928; ENSG00000175287. [Q5SRE7-2]
GeneIDi254295.
KEGGihsa:254295.
UCSCiuc004bwn.3. human. [Q5SRE7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK095000 mRNA. Translation: BAG52969.1.
AL672142 Genomic DNA. Translation: CAI10840.1. Sequence problems.
AL672142 Genomic DNA. Translation: CAI10842.1.
AL672142 Genomic DNA. Translation: CAI10843.1.
AL672142 Genomic DNA. Translation: CAO72146.1. Sequence problems.
AL672142 Genomic DNA. Translation: CAO72147.1. Sequence problems.
AL672142 Genomic DNA. Translation: CAQ77683.1.
CH471090 Genomic DNA. Translation: EAW87844.1.
CH471090 Genomic DNA. Translation: EAW87845.1.
CH471090 Genomic DNA. Translation: EAW87847.1.
BC009373 mRNA. Translation: AAH09373.1.
BC051300 mRNA. Translation: AAH51300.1.
BC053853 mRNA. Translation: AAH53853.1.
CCDSiCCDS43885.1. [Q5SRE7-1]
CCDS43886.1. [Q5SRE7-2]
CCDS6914.1. [Q5SRE7-3]
RefSeqiNP_001094346.1. NM_001100876.1. [Q5SRE7-1]
NP_001094347.1. NM_001100877.1. [Q5SRE7-2]
NP_777593.2. NM_174933.3. [Q5SRE7-3]
UniGeneiHs.709447.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2OPWX-ray1.90A1-291[»]
3OBZX-ray2.15A1-291[»]
ProteinModelPortaliQ5SRE7.
SMRiQ5SRE7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi129029. 3 interactors.
IntActiQ5SRE7. 2 interactors.
MINTiMINT-6768910.
STRINGi9606.ENSP00000309515.

PTM databases

iPTMnetiQ5SRE7.
PhosphoSitePlusiQ5SRE7.

Polymorphism and mutation databases

BioMutaiPHYHD1.
DMDMi166220781.

Proteomic databases

EPDiQ5SRE7.
MaxQBiQ5SRE7.
PaxDbiQ5SRE7.
PeptideAtlasiQ5SRE7.
PRIDEiQ5SRE7.

Protocols and materials databases

DNASUi254295.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000308941; ENSP00000309515; ENSG00000175287. [Q5SRE7-3]
ENST00000353176; ENSP00000340945; ENSG00000175287. [Q5SRE7-2]
ENST00000372592; ENSP00000361673; ENSG00000175287. [Q5SRE7-1]
ENST00000421063; ENSP00000409928; ENSG00000175287. [Q5SRE7-2]
GeneIDi254295.
KEGGihsa:254295.
UCSCiuc004bwn.3. human. [Q5SRE7-1]

Organism-specific databases

CTDi254295.
DisGeNETi254295.
GeneCardsiPHYHD1.
HGNCiHGNC:23396. PHYHD1.
HPAiHPA012115.
neXtProtiNX_Q5SRE7.
OpenTargetsiENSG00000175287.
PharmGKBiPA134959674.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3290. Eukaryota.
ENOG410XUSH. LUCA.
GeneTreeiENSGT00390000006287.
HOVERGENiHBG054973.
InParanoidiQ5SRE7.
OMAiSSTEKWC.
PhylomeDBiQ5SRE7.
TreeFamiTF300011.

Miscellaneous databases

ChiTaRSiPHYHD1. human.
EvolutionaryTraceiQ5SRE7.
GenomeRNAii254295.
PROiQ5SRE7.

Gene expression databases

BgeeiENSG00000175287.
CleanExiHS_PHYHD1.
ExpressionAtlasiQ5SRE7. baseline and differential.
GenevisibleiQ5SRE7. HS.

Family and domain databases

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

Entry informationi

Entry nameiPHYD1_HUMAN
AccessioniPrimary (citable) accession number: Q5SRE7
Secondary accession number(s): A6PWN9
, A6PWP0, B3KT57, B4E3X8, Q5SRE9, Q5SRF0, Q7Z623, Q7Z7P9, Q96GM4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: January 15, 2008
Last modified: November 2, 2016
This is version 99 of the entry and version 2 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 9
    Human chromosome 9: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. 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.