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Protein

Pentatricopeptide repeat-containing protein 1, mitochondrial

Gene

PTCD1

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

Functioni

Mitochondrial protein implicated in negative regulation of leucine tRNA levels, as well as negative regulation of mitochondria-encoded proteins and COX activity. Affects also the 3'-processing of mitochondrial tRNAs.1 Publication

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • tRNA binding Source: UniProtKB

GO - Biological processi

  • tRNA 3'-end processing Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

tRNA processing

Names & Taxonomyi

Protein namesi
Recommended name:
Pentatricopeptide repeat-containing protein 1, mitochondrial
Gene namesi
Name:PTCD1
Synonyms:KIAA0632
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:22198. PTCD1.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial matrix Source: UniProtKB
  • mitochondrion Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134877986.

Polymorphism and mutation databases

BioMutaiPTCD1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 700700Pentatricopeptide repeat-containing protein 1, mitochondrialPRO_0000097089Add
BLAST

Proteomic databases

EPDiO75127.
MaxQBiO75127.
PaxDbiO75127.
PRIDEiO75127.

PTM databases

iPTMnetiO75127.
PhosphoSiteiO75127.

Expressioni

Tissue specificityi

Abundant in testes, skeletal muscle and heart.1 Publication

Gene expression databases

BgeeiO75127.
CleanExiHS_PTCD1.
ExpressionAtlasiO75127. baseline and differential.
GenevisibleiO75127. HS.

Organism-specific databases

HPAiHPA020106.
HPA047679.

Interactioni

Subunit structurei

Associates with mitochondrial leucine tRNAs. Interacts with ELAC2.2 Publications

Protein-protein interaction databases

BioGridi117493. 27 interactions.
IntActiO75127. 5 interactions.
STRINGi9606.ENSP00000450995.

Structurei

3D structure databases

ProteinModelPortaliO75127.
SMRiO75127. Positions 146-317, 457-618.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati135 – 17137PPR 1Add
BLAST
Repeati172 – 20635PPR 2Add
BLAST
Repeati207 – 24539PPR 3Add
BLAST
Repeati246 – 28035PPR 4Add
BLAST
Repeati281 – 31737PPR 5Add
BLAST
Repeati318 – 35437PPR 6Add
BLAST
Repeati519 – 55335PPR 7Add
BLAST
Repeati554 – 58532PPR 8Add
BLAST
Repeati586 – 62035PPR 9Add
BLAST

Sequence similaritiesi

Belongs to the PTCD1 family.Curated
Contains 9 PPR (pentatricopeptide) repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG4092. Eukaryota.
KOG4197. Eukaryota.
ENOG410Z7Z7. LUCA.
GeneTreeiENSGT00390000015597.
HOGENOMiHOG000237315.
HOVERGENiHBG053748.
InParanoidiO75127.
KOiK17710.
OrthoDBiEOG7DZ8K5.
PhylomeDBiO75127.

Family and domain databases

InterProiIPR002885. Pentatricopeptide_repeat.
IPR033443. PPR_long.
[Graphical view]
PfamiPF13812. PPR_3. 1 hit.
PF17177. PPR_long. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00756. PPR. 1 hit.
PROSITEiPS51375. PPR. 7 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O75127-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDFVRLARLF ARARPMGLFI LQHLDPCRAR WAGGREGLMR PMWAPFSSSS
60 70 80 90 100
SQLPLGQERQ ENTGSLGSDP SHSNSTATQE EDEEEEESFG TLSDKYSSRR
110 120 130 140 150
LFRKSAAQFH NLRFGERRDE QMEPEPKLWR GRRNTPYWYF LQCKHLIKEG
160 170 180 190 200
KLVEALDLFE RQMLKEERLQ PMESNYTVLI GGCGRVGYLK KAFNLYNQMK
210 220 230 240 250
KRDLEPSDAT YTALFNVCAE SPWKDSALQS ALKLRQQLQA KNFELNLKTY
260 270 280 290 300
HALLKMAAKC ADLRMCLDVF KEIIHKGHVV TEETFSFLLM GCIQDKKTGF
310 320 330 340 350
RYALQVWRLM LSLGLQPSRD SYNLLLVAAR DCGLGDPQVA SELLLKPREE
360 370 380 390 400
ATVLQPPVSR QRPRRTAQAK AGNLMSAMLH VEALERQLFL EPSQALGPPE
410 420 430 440 450
PPEARVPGKA QPEVDTKAEP SHTAALTAVA LKPPPVELEV NLLTPGAVPP
460 470 480 490 500
TVVSFGTVTT PADRLALIGG LEGFLSKMAE HRQQPDIRTL TLLAEVVESG
510 520 530 540 550
SPAESLLLAL LDEHQVEADL TFFNTLVRKK SKLGDLEGAK ALLPVLAKRG
560 570 580 590 600
LVPNLQTFCN LAIGCHRPKD GLQLLTDMKK SQVTPNTHIY SALINAAIRK
610 620 630 640 650
LNYTYLISIL KDMKQNRVPV NEVVIRQLEF AAQYPPTFDR YQGKNTYLEK
660 670 680 690 700
IDGFRAYYKQ WLTVMPAEET PHPWQKFRTK PQGDQDTGKE ADDGCALGGR
Length:700
Mass (Da):78,856
Last modified:March 29, 2005 - v2
Checksum:iE5075DC65C3D40E0
GO

Sequence cautioni

The sequence BAA31607.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti505 – 5051S → F in AAH80580 (PubMed:12853948).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti356 – 3561P → L.
Corresponds to variant rs34714513 [ dbSNP | Ensembl ].
VAR_052936
Natural varianti620 – 6201V → G.
Corresponds to variant rs35633728 [ dbSNP | Ensembl ].
VAR_052937

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB014532 mRNA. Translation: BAA31607.1. Different initiation.
AC004922 Genomic DNA. No translation available.
AC073063 Genomic DNA. No translation available.
AC090113 Genomic DNA. No translation available.
BC003688 mRNA. Translation: AAH03688.2.
BC080580 mRNA. Translation: AAH80580.1.
BC103502 mRNA. Translation: AAI03503.1.
CCDSiCCDS34691.1.
PIRiT00383.
RefSeqiNP_056360.2. NM_015545.3.
UniGeneiHs.632313.
Hs.729925.

Genome annotation databases

EnsembliENST00000292478; ENSP00000292478; ENSG00000106246.
GeneIDi26024.
KEGGihsa:26024.
UCSCiuc003uqh.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB014532 mRNA. Translation: BAA31607.1. Different initiation.
AC004922 Genomic DNA. No translation available.
AC073063 Genomic DNA. No translation available.
AC090113 Genomic DNA. No translation available.
BC003688 mRNA. Translation: AAH03688.2.
BC080580 mRNA. Translation: AAH80580.1.
BC103502 mRNA. Translation: AAI03503.1.
CCDSiCCDS34691.1.
PIRiT00383.
RefSeqiNP_056360.2. NM_015545.3.
UniGeneiHs.632313.
Hs.729925.

3D structure databases

ProteinModelPortaliO75127.
SMRiO75127. Positions 146-317, 457-618.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117493. 27 interactions.
IntActiO75127. 5 interactions.
STRINGi9606.ENSP00000450995.

PTM databases

iPTMnetiO75127.
PhosphoSiteiO75127.

Polymorphism and mutation databases

BioMutaiPTCD1.

Proteomic databases

EPDiO75127.
MaxQBiO75127.
PaxDbiO75127.
PRIDEiO75127.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000292478; ENSP00000292478; ENSG00000106246.
GeneIDi26024.
KEGGihsa:26024.
UCSCiuc003uqh.4. human.

Organism-specific databases

CTDi26024.
GeneCardsiPTCD1.
HGNCiHGNC:22198. PTCD1.
HPAiHPA020106.
HPA047679.
MIMi614774. gene.
neXtProtiNX_O75127.
PharmGKBiPA134877986.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4092. Eukaryota.
KOG4197. Eukaryota.
ENOG410Z7Z7. LUCA.
GeneTreeiENSGT00390000015597.
HOGENOMiHOG000237315.
HOVERGENiHBG053748.
InParanoidiO75127.
KOiK17710.
OrthoDBiEOG7DZ8K5.
PhylomeDBiO75127.

Miscellaneous databases

ChiTaRSiPTCD1. human.
GenomeRNAii26024.
PROiO75127.
SOURCEiSearch...

Gene expression databases

BgeeiO75127.
CleanExiHS_PTCD1.
ExpressionAtlasiO75127. baseline and differential.
GenevisibleiO75127. HS.

Family and domain databases

InterProiIPR002885. Pentatricopeptide_repeat.
IPR033443. PPR_long.
[Graphical view]
PfamiPF13812. PPR_3. 1 hit.
PF17177. PPR_long. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00756. PPR. 1 hit.
PROSITEiPS51375. PPR. 7 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro."
    Ishikawa K., Nagase T., Suyama M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 5:169-176(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  2. "The DNA sequence of human chromosome 7."
    Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L.
    , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
    Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Ovary and Placenta.
  4. "Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells."
    Rackham O., Davies S.M., Shearwood A.M., Hamilton K.L., Whelan J., Filipovska A.
    Nucleic Acids Res. 37:5859-5867(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY, SUBUNIT, SUBCELLULAR LOCATION.
  5. "RNA processing in human mitochondria."
    Sanchez M.I., Mercer T.R., Davies S.M., Shearwood A.M., Nygard K.K., Richman T.R., Mattick J.S., Rackham O., Filipovska A.
    Cell Cycle 10:2904-2916(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, SUBUNIT, INTERACTION WITH ELAC2, FUNCTION.

Entry informationi

Entry nameiPTCD1_HUMAN
AccessioniPrimary (citable) accession number: O75127
Secondary accession number(s): Q3ZB78, Q66K60, Q9UDV2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: March 29, 2005
Last modified: June 8, 2016
This is version 114 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: 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. 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.