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Protein

Pentatricopeptide repeat domain-containing protein 3, mitochondrial

Gene

PTCD3

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

Functioni

Mitochondrial RNA-binding protein that has a role in mitochondrial translation.1 Publication

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • ribosomal small subunit binding Source: UniProtKB
  • rRNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Translation regulation

Keywords - Ligandi

RNA-binding, rRNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-5368286. Mitochondrial translation initiation.
R-HSA-5389840. Mitochondrial translation elongation.
R-HSA-5419276. Mitochondrial translation termination.

Names & Taxonomyi

Protein namesi
Recommended name:
Pentatricopeptide repeat domain-containing protein 3, mitochondrial
Alternative name(s):
28S ribosomal protein S39, mitochondrial
Short name:
MRP-S39
Transformation-related gene 15 protein
Short name:
TRG-15
Gene namesi
Name:PTCD3
Synonyms:MRPS39
ORF Names:TRG15
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:24717. PTCD3.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial inner membrane Source: Reactome
  • mitochondrion Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000132300.
PharmGKBiPA147357465.

Polymorphism and mutation databases

BioMutaiPTCD3.
DMDMi74731633.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 37MitochondrionSequence analysisAdd BLAST37
ChainiPRO_000030502838 – 689Pentatricopeptide repeat domain-containing protein 3, mitochondrialAdd BLAST652

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei126N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ96EY7.
MaxQBiQ96EY7.
PaxDbiQ96EY7.
PeptideAtlasiQ96EY7.
PRIDEiQ96EY7.

PTM databases

iPTMnetiQ96EY7.
PhosphoSitePlusiQ96EY7.
SwissPalmiQ96EY7.

Expressioni

Tissue specificityi

Abundant in testes, skeletal muscle and heart tissue.1 Publication

Gene expression databases

BgeeiENSG00000132300.
CleanExiHS_PTCD3.
ExpressionAtlasiQ96EY7. baseline and differential.
GenevisibleiQ96EY7. HS.

Organism-specific databases

HPAiHPA041154.
HPA041382.

Interactioni

Subunit structurei

Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins. Associated with the 12S mitochondrial rRNA (12S mt-rRNA).2 Publications

Protein-protein interaction databases

BioGridi120366. 87 interactors.
IntActiQ96EY7. 29 interactors.
MINTiMINT-1383816.
STRINGi9606.ENSP00000254630.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J9Melectron microscopy3.50A41-689[»]
ProteinModelPortaliQ96EY7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati149 – 183PPR 1Add BLAST35
Repeati184 – 219PPR 2Add BLAST36
Repeati255 – 289PPR 3Add BLAST35
Repeati290 – 330PPR 4Add BLAST41
Repeati331 – 367PPR 5Add BLAST37
Repeati368 – 409PPR 6Add BLAST42
Repeati412 – 446PPR 7Add BLAST35
Repeati454 – 488PPR 8Add BLAST35
Repeati489 – 523PPR 9Add BLAST35
Repeati572 – 606PPR 10Add BLAST35

Sequence similaritiesi

Belongs to the PTCD3 family.Curated
Contains 10 PPR (pentatricopeptide) repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Transit peptide

Phylogenomic databases

eggNOGiKOG4422. Eukaryota.
ENOG410XNQS. LUCA.
GeneTreeiENSGT00390000016876.
HOVERGENiHBG068809.
InParanoidiQ96EY7.
KOiK17659.
OMAiAPHYKYH.
OrthoDBiEOG091G03F0.
PhylomeDBiQ96EY7.
TreeFamiTF320158.

Family and domain databases

InterProiIPR002885. Pentatricopeptide_repeat.
[Graphical view]
PfamiPF13041. PPR_2. 1 hit.
PF13812. PPR_3. 1 hit.
[Graphical view]
PROSITEiPS51375. PPR. 4 hits.
[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: Q96EY7-1) [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
MAVVSAVRWL GLRSRLGQPL TGRRAGLCEQ ARSCRFYSGS ATLSKVEGTD
60 70 80 90 100
VTGIEEVVIP KKKTWDKVAV LQALASTVNR DTTAVPYVFQ DDPYLMPASS
110 120 130 140 150
LESRSFLLAK KSGENVAKFI INSYPKYFQK DIAEPHIPCL MPEYFEPQIK
160 170 180 190 200
DISEAALKER IELRKVKASV DMFDQLLQAG TTVSLETTNS LLDLLCYYGD
210 220 230 240 250
QEPSTDYHFQ QTGQSEALEE ENDETSRRKA GHQFGVTWRA KNNAERIFSL
260 270 280 290 300
MPEKNEHSYC TMIRGMVKHR AYEQALNLYT ELLNNRLHAD VYTFNALIEA
310 320 330 340 350
TVCAINEKFE EKWSKILELL RHMVAQKVKP NLQTFNTILK CLRRFHVFAR
360 370 380 390 400
SPALQVLREM KAIGIEPSLA TYHHIIRLFD QPGDPLKRSS FIIYDIMNEL
410 420 430 440 450
MGKRFSPKDP DDDKFFQSAM SICSSLRDLE LAYQVHGLLK TGDNWKFIGP
460 470 480 490 500
DQHRNFYYSK FFDLICLMEQ IDVTLKWYED LIPSAYFPHS QTMIHLLQAL
510 520 530 540 550
DVANRLEVIP KIWKDSKEYG HTFRSDLREE ILMLMARDKH PPELQVAFAD
560 570 580 590 600
CAADIKSAYE SQPIRQTAQD WPATSLNCIA ILFLRAGRTQ EAWKMLGLFR
610 620 630 640 650
KHNKIPRSEL LNELMDSAKV SNSPSQAIEV VELASAFSLP ICEGLTQRVM
660 670 680
SDFAINQEQK EALSNLTALT SDSDTDSSSD SDSDTSEGK
Length:689
Mass (Da):78,550
Last modified:November 23, 2004 - v3
Checksum:i901DBE1FF3A2E0B9
GO
Isoform 2 (identifier: Q96EY7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-409: Missing.
     410-413: PDDD → MMAY

Note: No experimental confirmation available.
Show »
Length:280
Mass (Da):31,863
Checksum:i013682E2D4C7330A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti400L → S in AAQ18037 (Ref. 6) Curated1
Sequence conflicti488P → L in AAH01758 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0351542A → V.Corresponds to variant rs13393659dbSNPEnsembl.1
Natural variantiVAR_035155681S → G.Corresponds to variant rs2241433dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0281911 – 409Missing in isoform 2. 1 PublicationAdd BLAST409
Alternative sequenceiVSP_028192410 – 413PDDD → MMAY in isoform 2. 1 Publication4

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000765 mRNA. Translation: BAA91370.1.
AC009309 Genomic DNA. No translation available.
CH471053 Genomic DNA. Translation: EAW99464.1.
CH471053 Genomic DNA. Translation: EAW99465.1.
BC001758 mRNA. Translation: AAH01758.3.
BC011832 mRNA. Translation: AAH11832.3.
AL832520 mRNA. Translation: CAH56345.1.
AY277598 mRNA. Translation: AAQ18037.1.
CCDSiCCDS33235.1. [Q96EY7-1]
RefSeqiNP_060422.4. NM_017952.5. [Q96EY7-1]
UniGeneiHs.323489.
Hs.623885.

Genome annotation databases

EnsembliENST00000254630; ENSP00000254630; ENSG00000132300. [Q96EY7-1]
GeneIDi55037.
KEGGihsa:55037.
UCSCiuc002sqw.2. human. [Q96EY7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000765 mRNA. Translation: BAA91370.1.
AC009309 Genomic DNA. No translation available.
CH471053 Genomic DNA. Translation: EAW99464.1.
CH471053 Genomic DNA. Translation: EAW99465.1.
BC001758 mRNA. Translation: AAH01758.3.
BC011832 mRNA. Translation: AAH11832.3.
AL832520 mRNA. Translation: CAH56345.1.
AY277598 mRNA. Translation: AAQ18037.1.
CCDSiCCDS33235.1. [Q96EY7-1]
RefSeqiNP_060422.4. NM_017952.5. [Q96EY7-1]
UniGeneiHs.323489.
Hs.623885.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J9Melectron microscopy3.50A41-689[»]
ProteinModelPortaliQ96EY7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120366. 87 interactors.
IntActiQ96EY7. 29 interactors.
MINTiMINT-1383816.
STRINGi9606.ENSP00000254630.

PTM databases

iPTMnetiQ96EY7.
PhosphoSitePlusiQ96EY7.
SwissPalmiQ96EY7.

Polymorphism and mutation databases

BioMutaiPTCD3.
DMDMi74731633.

Proteomic databases

EPDiQ96EY7.
MaxQBiQ96EY7.
PaxDbiQ96EY7.
PeptideAtlasiQ96EY7.
PRIDEiQ96EY7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254630; ENSP00000254630; ENSG00000132300. [Q96EY7-1]
GeneIDi55037.
KEGGihsa:55037.
UCSCiuc002sqw.2. human. [Q96EY7-1]

Organism-specific databases

CTDi55037.
GeneCardsiPTCD3.
HGNCiHGNC:24717. PTCD3.
HPAiHPA041154.
HPA041382.
MIMi614918. gene.
neXtProtiNX_Q96EY7.
OpenTargetsiENSG00000132300.
PharmGKBiPA147357465.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4422. Eukaryota.
ENOG410XNQS. LUCA.
GeneTreeiENSGT00390000016876.
HOVERGENiHBG068809.
InParanoidiQ96EY7.
KOiK17659.
OMAiAPHYKYH.
OrthoDBiEOG091G03F0.
PhylomeDBiQ96EY7.
TreeFamiTF320158.

Enzyme and pathway databases

ReactomeiR-HSA-5368286. Mitochondrial translation initiation.
R-HSA-5389840. Mitochondrial translation elongation.
R-HSA-5419276. Mitochondrial translation termination.

Miscellaneous databases

GenomeRNAii55037.
PROiQ96EY7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000132300.
CleanExiHS_PTCD3.
ExpressionAtlasiQ96EY7. baseline and differential.
GenevisibleiQ96EY7. HS.

Family and domain databases

InterProiIPR002885. Pentatricopeptide_repeat.
[Graphical view]
PfamiPF13041. PPR_2. 1 hit.
PF13812. PPR_3. 1 hit.
[Graphical view]
PROSITEiPS51375. PPR. 4 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPTCD3_HUMAN
AccessioniPrimary (citable) accession number: Q96EY7
Secondary accession number(s): A6NHD2
, D6W5M1, Q597H0, Q658Y9, Q9BUZ8, Q9NWL0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 2, 2007
Last sequence update: November 23, 2004
Last modified: November 2, 2016
This is version 129 of the entry and version 3 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 2
    Human chromosome 2: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.