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Protein

Pentatricopeptide repeat-containing protein 1, mitochondrial

Gene

Ptcd1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at transcript 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.By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

tRNA processing

Names & Taxonomyi

Protein namesi
Recommended name:
Pentatricopeptide repeat-containing protein 1, mitochondrial
Gene namesi
Name:Ptcd1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 12

Organism-specific databases

RGDi1311473. Ptcd1.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 686686Pentatricopeptide repeat-containing protein 1, mitochondrialPRO_0000420158Add
BLAST

Proteomic databases

PaxDbiA2VD13.
PRIDEiA2VD13.

Expressioni

Gene expression databases

ExpressionAtlasiA2VD13. baseline.
GenevisibleiA2VD13. RN.

Interactioni

Subunit structurei

Associates with mitochondrial leucine tRNAs. Interacts with ELAC2.By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000057644.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati124 – 16037PPR 1Add
BLAST
Repeati161 – 19535PPR 2Add
BLAST
Repeati196 – 23439PPR 3Add
BLAST
Repeati235 – 26935PPR 4Add
BLAST
Repeati270 – 30637PPR 5Add
BLAST
Repeati508 – 54235PPR 6Add
BLAST
Repeati575 – 60935PPR 7Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi46 – 516Poly-Ser
Compositional biasi71 – 766Poly-Glu
Compositional biasi109 – 1146Poly-Glu

Sequence similaritiesi

Belongs to the PTCD1 family.Curated
Contains 7 PPR (pentatricopeptide) repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG4197. Eukaryota.
ENOG410Z7Z7. LUCA.
GeneTreeiENSGT00390000015597.
HOGENOMiHOG000237315.
HOVERGENiHBG053748.
InParanoidiA2VD13.
TreeFamiTF324792.

Family and domain databases

InterProiIPR002885. Pentatricopeptide_repeat.
[Graphical view]
PfamiPF13041. PPR_2. 1 hit.
PF13812. PPR_3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00756. PPR. 1 hit.
PROSITEiPS51375. PPR. 7 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A2VD13-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDLLRLSRLF SGPHPIGLSV LQRLDLLRST QWTGGREGPA WLRAASCSSS
60 70 80 90 100
SHQKRMSSLC SDSSTPVAPQ EEEEEESFGT LSEKFSSRRI FHKSTAQLYN
110 120 130 140 150
LKLKEQGVEE EELEPRLRQG GRNTPYWYFL QCKRLLKEGK LAEALDLFER
160 170 180 190 200
QMLKEERLQP LECNYTVLIG GCGRVGYLKK AFRLFNDMKK RDLEPSDATY
210 220 230 240 250
TALFNVCAES PWKDSALQSA LKLRQQLQAQ NFQLNLKTYH ALLKVAAKCA
260 270 280 290 300
DLRVCLEVFK EIIQKGHAVT EETFCFLLMG CIQDKKTGFR QAMQVWRQML
310 320 330 340 350
SLGIKPSRHG YNLLLGAARD CGLGDPEVAS RLLLTSQEET ILLQPPTGRR
360 370 380 390 400
LAGGKVQAKT RHGVSVKHVE ALERQLFLEP SHKLEGPPAF PEARETSRTQ
410 420 430 440 450
PEVETKAEPG HMGALAPLAL KPPDLELQVN LLSLGALSPA VVSFGTVATP
460 470 480 490 500
ADRLALMGGL EGFLGKMAEH RLQPDIKTLT LLAEVVEPGS PAESSLLSIL
510 520 530 540 550
DRHRVEADIT FFNTLIRKKS KLGDLEGAKA LLPILAKKGI VPNLRTFCNL
560 570 580 590 600
AIGCHRPRDG MQLLADMKKS QVTPNTHIYS TLINAALKKL DYTYLISILK
610 620 630 640 650
DMRRNSVPVN EVVIRQLEFA AQYPPTFDRY KEKNTYLEKI DGFRAYYKQW
660 670 680
LKVMPAEEPP HPWQEFRDKP VRNQVITENA GGLRDG
Length:686
Mass (Da):77,121
Last modified:March 20, 2007 - v1
Checksum:i626472E097FBCA11
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR06070420 Genomic DNA. No translation available.
BC129116 mRNA. Translation: AAI29117.1.
RefSeqiXP_006248933.1. XM_006248871.1.
UniGeneiRn.105071.

Genome annotation databases

EnsembliENSRNOT00000076896; ENSRNOP00000068093; ENSRNOG00000000987.
GeneIDi304278.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR06070420 Genomic DNA. No translation available.
BC129116 mRNA. Translation: AAI29117.1.
RefSeqiXP_006248933.1. XM_006248871.1.
UniGeneiRn.105071.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000057644.

Proteomic databases

PaxDbiA2VD13.
PRIDEiA2VD13.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000076896; ENSRNOP00000068093; ENSRNOG00000000987.
GeneIDi304278.

Organism-specific databases

CTDi26024.
RGDi1311473. Ptcd1.

Phylogenomic databases

eggNOGiKOG4197. Eukaryota.
ENOG410Z7Z7. LUCA.
GeneTreeiENSGT00390000015597.
HOGENOMiHOG000237315.
HOVERGENiHBG053748.
InParanoidiA2VD13.
TreeFamiTF324792.

Miscellaneous databases

PROiA2VD13.

Gene expression databases

ExpressionAtlasiA2VD13. baseline.
GenevisibleiA2VD13. RN.

Family and domain databases

InterProiIPR002885. Pentatricopeptide_repeat.
[Graphical view]
PfamiPF13041. PPR_2. 1 hit.
PF13812. PPR_3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00756. PPR. 1 hit.
PROSITEiPS51375. PPR. 7 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
    Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
    , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
    Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  2. "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: Testis.
  3. "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: SUBCELLULAR LOCATION.

Entry informationi

Entry nameiPTCD1_RAT
AccessioniPrimary (citable) accession number: A2VD13
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2012
Last sequence update: March 20, 2007
Last modified: June 8, 2016
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.