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Protein

Decaprenyl-diphosphate synthase subunit 1

Gene

PDSS1

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

Functioni

Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10.1 Publication

Catalytic activityi

(2E,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-decaprenyl diphosphate.1 Publication

Cofactori

Mg2+By similarityNote: Binds 3 Mg2+ ions per subunit.By similarity

Pathwayi: ubiquinone biosynthesis

This protein is involved in the pathway ubiquinone biosynthesis, which is part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the pathway ubiquinone biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei134Isopentenyl diphosphateBy similarity1
Binding sitei137Isopentenyl diphosphateBy similarity1
Binding sitei173Isopentenyl diphosphateBy similarity1
Metal bindingi180Magnesium 1By similarity1
Metal bindingi180Magnesium 2By similarity1
Metal bindingi184Magnesium 1By similarity1
Metal bindingi184Magnesium 2By similarity1
Binding sitei189Polyprenyl diphosphateBy similarity1
Binding sitei190Isopentenyl diphosphateBy similarity1
Binding sitei266Polyprenyl diphosphateBy similarity1
Binding sitei267Polyprenyl diphosphateBy similarity1
Binding sitei304Polyprenyl diphosphateBy similarity1
Metal bindingi307Magnesium 3By similarity1
Binding sitei321Polyprenyl diphosphateBy similarity1

GO - Molecular functioni

GO - Biological processi

  • isoprenoid biosynthetic process Source: HGNC
  • protein heterotetramerization Source: Ensembl
  • ubiquinone biosynthetic process Source: HGNC
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Isoprene biosynthesis, Ubiquinone biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:HS07530-MONOMER.
ZFISH:HS07530-MONOMER.
BRENDAi2.5.1.91. 2681.
ReactomeiR-HSA-2142789. Ubiquinol biosynthesis.
UniPathwayiUPA00232.

Names & Taxonomyi

Protein namesi
Recommended name:
Decaprenyl-diphosphate synthase subunit 1 (EC:2.5.1.91)
Alternative name(s):
All-trans-decaprenyl-diphosphate synthase subunit 1
Decaprenyl pyrophosphate synthase subunit 1
Trans-prenyltransferase 1
Short name:
TPT 1
Gene namesi
Name:PDSS1
Synonyms:DPS1, TPRT
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:17759. PDSS1.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial matrix Source: Reactome
  • transferase complex Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Coenzyme Q10 deficiency, primary, 2 (COQ10D2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive multisystem disorder characterized by early-onset deafness, optic atrophy, mild mental retardation, peripheral neuropathy, obesity, livedo reticularis, and cardiac valvulopathy.
See also OMIM:614651
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_034879308D → E in COQ10D2. 1 PublicationCorresponds to variant rs119463988dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi23590.
MalaCardsiPDSS1.
MIMi614651. phenotype.
OpenTargetsiENSG00000148459.
Orphaneti254898. Deafness - encephaloneuropathy - obesity - valvulopathy.
PharmGKBiPA134982512.

Polymorphism and mutation databases

BioMutaiPDSS1.
DMDMi74744657.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001239751 – 415Decaprenyl-diphosphate synthase subunit 1Add BLAST415

Proteomic databases

EPDiQ5T2R2.
MaxQBiQ5T2R2.
PaxDbiQ5T2R2.
PeptideAtlasiQ5T2R2.
PRIDEiQ5T2R2.

PTM databases

iPTMnetiQ5T2R2.
PhosphoSitePlusiQ5T2R2.

Expressioni

Gene expression databases

BgeeiENSG00000148459.
CleanExiHS_PDSS1.
ExpressionAtlasiQ5T2R2. baseline and differential.
GenevisibleiQ5T2R2. HS.

Organism-specific databases

HPAiHPA038032.
HPA042741.

Interactioni

Subunit structurei

Heterotetramer of 2 DPS1/TPRT and 2 DLP1 subunits.1 Publication

GO - Molecular functioni

  • protein heterodimerization activity Source: HGNC

Protein-protein interaction databases

BioGridi117125. 7 interactors.
IntActiQ5T2R2. 1 interactor.
STRINGi9606.ENSP00000365388.

Structurei

3D structure databases

ProteinModelPortaliQ5T2R2.
SMRiQ5T2R2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the FPP/GGPP synthase family.Curated

Phylogenomic databases

eggNOGiKOG0776. Eukaryota.
COG0142. LUCA.
GeneTreeiENSGT00530000063378.
HOGENOMiHOG000009104.
HOVERGENiHBG054389.
InParanoidiQ5T2R2.
KOiK12504.
OMAiFAQASWH.
OrthoDBiEOG091G1BWC.
PhylomeDBiQ5T2R2.
TreeFamiTF313548.

Family and domain databases

Gene3Di1.10.600.10. 1 hit.
InterProiIPR008949. Isoprenoid_synthase_dom.
IPR000092. Polyprenyl_synt.
IPR033749. Polyprenyl_synt_CS.
[Graphical view]
PfamiPF00348. polyprenyl_synt. 1 hit.
[Graphical view]
SUPFAMiSSF48576. SSF48576. 1 hit.
PROSITEiPS00723. POLYPRENYL_SYNTHASE_1. 1 hit.
PS00444. POLYPRENYL_SYNTHASE_2. 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: Q5T2R2-1) [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
MASRWWRWRR GCSWKPAARS PGPGSPGRAG PLGPSAAAEV RAQVHRRKGL
60 70 80 90 100
DLSQIPYINL VKHLTSACPN VCRISRFHHT TPDSKTHSGE KYTDPFKLGW
110 120 130 140 150
RDLKGLYEDI RKELLISTSE LKEMSEYYFD GKGKAFRPII VALMARACNI
160 170 180 190 200
HHNNSRHVQA SQRAIALIAE MIHTASLVHD DVIDDASSRR GKHTVNKIWG
210 220 230 240 250
EKKAVLAGDL ILSAASIALA RIGNTTVISI LTQVIEDLVR GEFLQLGSKE
260 270 280 290 300
NENERFAHYL EKTFKKTASL IANSCKAVSV LGCPDPVVHE IAYQYGKNVG
310 320 330 340 350
IAFQLIDDVL DFTSCSDQMG KPTSADLKLG LATGPVLFAC QQFPEMNAMI
360 370 380 390 400
MRRFSLPGDV DRARQYVLQS DGVQQTTYLA QQYCHEAIRE ISKLRPSPER
410
DALIQLSEIV LTRDK
Length:415
Mass (Da):46,261
Last modified:December 21, 2004 - v1
Checksum:iF0B073C75CBD06D2
GO
Isoform 2 (identifier: Q5T2R2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     279-415: SVLGCPDPVV...LSEIVLTRDK → FPRNECYDHATVQFAWRCRQSSTVCTTE

Note: No experimental confirmation available.
Show »
Length:306
Mass (Da):34,304
Checksum:iD5195700E8AFF902
GO
Isoform 3 (identifier: Q5T2R2-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-42: MASRWWRWRRGCSWKPAARSPGPGSPGRAGPLGPSAAAEVRA → MPA

Show »
Length:376
Mass (Da):42,089
Checksum:iBB32C9961B92ED00
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti30G → V in AAH63635 (PubMed:15489334).Curated1
Sequence conflicti44V → A in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti47R → Q in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti58I → F in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti66S → P in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti72 – 73CR → YS in AAD28559 (PubMed:10972372).Curated2
Sequence conflicti76R → Q in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti83D → Y in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti109D → G in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti114L → P in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti119S → T in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti124M → I in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti131G → V in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti142A → V in AAD28559 (PubMed:10972372).Curated1
Sequence conflicti186A → V in BAD97134 (Ref. 3) Curated1
Sequence conflicti298N → D in BAD97134 (Ref. 3) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_034879308D → E in COQ10D2. 1 PublicationCorresponds to variant rs119463988dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0171001 – 42MASRW…AEVRA → MPA in isoform 3. 1 PublicationAdd BLAST42
Alternative sequenceiVSP_017101279 – 415SVLGC…LTRDK → FPRNECYDHATVQFAWRCRQ SSTVCTTE in isoform 2. 1 PublicationAdd BLAST137

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF118395 mRNA. Translation: AAD28559.1.
AB210838 mRNA. Translation: BAE48216.1.
AK223414 mRNA. Translation: BAD97134.1.
AL390961 Genomic DNA. Translation: CAI17280.1.
BC049211 mRNA. Translation: AAH49211.1.
BC063635 mRNA. Translation: AAH63635.1.
CCDSiCCDS31168.1. [Q5T2R2-1]
RefSeqiNP_001308907.1. NM_001321978.1. [Q5T2R2-2]
NP_055132.2. NM_014317.4. [Q5T2R2-1]
UniGeneiHs.558468.

Genome annotation databases

EnsembliENST00000376215; ENSP00000365388; ENSG00000148459. [Q5T2R2-1]
GeneIDi23590.
KEGGihsa:23590.
UCSCiuc001isv.4. human. [Q5T2R2-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF118395 mRNA. Translation: AAD28559.1.
AB210838 mRNA. Translation: BAE48216.1.
AK223414 mRNA. Translation: BAD97134.1.
AL390961 Genomic DNA. Translation: CAI17280.1.
BC049211 mRNA. Translation: AAH49211.1.
BC063635 mRNA. Translation: AAH63635.1.
CCDSiCCDS31168.1. [Q5T2R2-1]
RefSeqiNP_001308907.1. NM_001321978.1. [Q5T2R2-2]
NP_055132.2. NM_014317.4. [Q5T2R2-1]
UniGeneiHs.558468.

3D structure databases

ProteinModelPortaliQ5T2R2.
SMRiQ5T2R2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117125. 7 interactors.
IntActiQ5T2R2. 1 interactor.
STRINGi9606.ENSP00000365388.

PTM databases

iPTMnetiQ5T2R2.
PhosphoSitePlusiQ5T2R2.

Polymorphism and mutation databases

BioMutaiPDSS1.
DMDMi74744657.

Proteomic databases

EPDiQ5T2R2.
MaxQBiQ5T2R2.
PaxDbiQ5T2R2.
PeptideAtlasiQ5T2R2.
PRIDEiQ5T2R2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000376215; ENSP00000365388; ENSG00000148459. [Q5T2R2-1]
GeneIDi23590.
KEGGihsa:23590.
UCSCiuc001isv.4. human. [Q5T2R2-1]

Organism-specific databases

CTDi23590.
DisGeNETi23590.
GeneCardsiPDSS1.
HGNCiHGNC:17759. PDSS1.
HPAiHPA038032.
HPA042741.
MalaCardsiPDSS1.
MIMi607429. gene.
614651. phenotype.
neXtProtiNX_Q5T2R2.
OpenTargetsiENSG00000148459.
Orphaneti254898. Deafness - encephaloneuropathy - obesity - valvulopathy.
PharmGKBiPA134982512.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0776. Eukaryota.
COG0142. LUCA.
GeneTreeiENSGT00530000063378.
HOGENOMiHOG000009104.
HOVERGENiHBG054389.
InParanoidiQ5T2R2.
KOiK12504.
OMAiFAQASWH.
OrthoDBiEOG091G1BWC.
PhylomeDBiQ5T2R2.
TreeFamiTF313548.

Enzyme and pathway databases

UniPathwayiUPA00232.
BioCyciMetaCyc:HS07530-MONOMER.
ZFISH:HS07530-MONOMER.
BRENDAi2.5.1.91. 2681.
ReactomeiR-HSA-2142789. Ubiquinol biosynthesis.

Miscellaneous databases

ChiTaRSiPDSS1. human.
GeneWikiiPDSS1.
GenomeRNAii23590.
PROiQ5T2R2.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000148459.
CleanExiHS_PDSS1.
ExpressionAtlasiQ5T2R2. baseline and differential.
GenevisibleiQ5T2R2. HS.

Family and domain databases

Gene3Di1.10.600.10. 1 hit.
InterProiIPR008949. Isoprenoid_synthase_dom.
IPR000092. Polyprenyl_synt.
IPR033749. Polyprenyl_synt_CS.
[Graphical view]
PfamiPF00348. polyprenyl_synt. 1 hit.
[Graphical view]
SUPFAMiSSF48576. SSF48576. 1 hit.
PROSITEiPS00723. POLYPRENYL_SYNTHASE_1. 1 hit.
PS00444. POLYPRENYL_SYNTHASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPS1_HUMAN
AccessioniPrimary (citable) accession number: Q5T2R2
Secondary accession number(s): Q53F75
, Q6P473, Q86WQ8, Q9Y2W5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: December 21, 2004
Last modified: November 30, 2016
This is version 119 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

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. 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.