RMD9_YEAST
ID RMD9_YEAST Reviewed; 646 AA.
AC P53140; D6VU39; Q66RA9;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=RNA-binding protein RMD9, mitochondrial {ECO:0000305};
DE AltName: Full=Dodecamer binding protein {ECO:0000303|PubMed:10441495};
DE Short=DBP {ECO:0000303|PubMed:10441495};
DE AltName: Full=Required for meiotic nuclear division protein 9;
DE Flags: Precursor;
GN Name=RMD9 {ECO:0000303|PubMed:17194787}; OrderedLocusNames=YGL107C;
GN ORFNames=G3075;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9046090;
RX DOI=10.1002/(sici)1097-0061(199701)13:1<85::aid-yea53>3.0.co;2-e;
RA Paoluzi S., Minenkova O., Castagnoli L.;
RT "The genes encoding the transcription factor yTAFII60, the G4p1 protein and
RT a putative glucose transporter are contained in a 12.3 kb DNA fragment on
RT the left arm of Saccharomyces cerevisiae chromosome VII.";
RL Yeast 13:85-91(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP PROTEIN SEQUENCE OF 52-56, X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) OF 51-646
RP IN COMPLEX WITH RNA, AND FUNCTION.
RX PubMed=33876744; DOI=10.1073/pnas.2009329118;
RA Hillen H.S., Markov D.A., Wojtas I.D., Hofmann K.B., Lidschreiber M.,
RA Cowan A.T., Jones J.L., Temiakov D., Cramer P., Anikin M.;
RT "The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric
RT element in the 3'-UTRs of yeast mitochondrial mRNAs.";
RL Proc. Natl. Acad. Sci. U.S.A. 118:0-0(2021).
RN [6]
RP FUNCTION, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=10441495; DOI=10.1006/bbrc.1999.1085;
RA Li H., Zassenhaus H.P.;
RT "Purification and characterization of an RNA dodecamer sequence binding
RT protein from mitochondria of Saccharomyces cerevisiae.";
RL Biochem. Biophys. Res. Commun. 261:740-745(1999).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND PHOSPHORYLATION.
RX PubMed=10905425; DOI=10.1007/s002940000117;
RA Li H., Zassenhaus H.P.;
RT "Phosphorylation is required for high-affinity binding of DBP, a yeast
RT mitochondrial site-specific RNA binding protein.";
RL Curr. Genet. 37:356-363(2000).
RN [8]
RP DISRUPTION PHENOTYPE.
RX PubMed=12586695; DOI=10.1093/genetics/163.1.47;
RA Enyenihi A.H., Saunders W.S.;
RT "Large-scale functional genomic analysis of sporulation and meiosis in
RT Saccharomyces cerevisiae.";
RL Genetics 163:47-54(2003).
RN [9]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 76625 / YPH499;
RX PubMed=14576278; DOI=10.1073/pnas.2135385100;
RA Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E.,
RA Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P.,
RA Pfanner N., Meisinger C.;
RT "The proteome of Saccharomyces cerevisiae mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
RN [12]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=17194787; DOI=10.1534/genetics.106.063883;
RA Nouet C., Bourens M., Hlavacek O., Marsy S., Lemaire C., Dujardin G.;
RT "Rmd9p controls the processing/stability of mitochondrial mRNAs and its
RT overexpression compensates for a partial deficiency of oxa1p in
RT Saccharomyces cerevisiae.";
RL Genetics 175:1105-1115(2007).
RN [13]
RP FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF VAL-363.
RX PubMed=17194786; DOI=10.1534/genetics.106.064576;
RA Williams E.H., Butler C.A., Bonnefoy N., Fox T.D.;
RT "Translation initiation in Saccharomyces cerevisiae mitochondria:
RT functional interactions among mitochondrial ribosomal protein Rsm28p,
RT initiation factor 2, methionyl-tRNA-formyltransferase and novel protein
RT Rmd9p.";
RL Genetics 175:1117-1126(2007).
CC -!- FUNCTION: Binds the RNA motif 5'-AAUAA[U/C]AUUCUU-3' in the 3'-UTR of
CC mitochondrial mRNAs (PubMed:33876744, PubMed:10441495,
CC PubMed:10905425). Involved in the processing or stability of
CC mitochondrial mRNAs (PubMed:33876744, PubMed:17194787,
CC PubMed:17194786). {ECO:0000269|PubMed:10441495,
CC ECO:0000269|PubMed:10905425, ECO:0000269|PubMed:17194786,
CC ECO:0000269|PubMed:17194787, ECO:0000269|PubMed:33876744}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:10441495}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:10441495, ECO:0000269|PubMed:10905425,
CC ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:14576278,
CC ECO:0000269|PubMed:17194786, ECO:0000269|PubMed:17194787}; Peripheral
CC membrane protein {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:14576278, ECO:0000269|PubMed:17194786,
CC ECO:0000269|PubMed:17194787}; Matrix side {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:14576278, ECO:0000269|PubMed:17194786,
CC ECO:0000269|PubMed:17194787}.
CC -!- PTM: Phosphorylated (PubMed:10905425). Phosphorylation promotes binding
CC to RNA (PubMed:10905425). {ECO:0000269|PubMed:10905425}.
CC -!- DISRUPTION PHENOTYPE: Abnormal meiosis. {ECO:0000269|PubMed:12586695}.
CC -!- MISCELLANEOUS: Present with 4800 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RMD9 family. {ECO:0000305}.
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DR EMBL; X97644; CAA66245.1; -; Genomic_DNA.
DR EMBL; Z72629; CAA96814.1; -; Genomic_DNA.
DR EMBL; AY723808; AAU09725.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08000.1; -; Genomic_DNA.
DR PIR; S64115; S64115.
DR RefSeq; NP_011408.1; NM_001180972.1.
DR PDB; 7A9W; X-ray; 2.55 A; A=51-646.
DR PDB; 7A9X; X-ray; 2.45 A; A=51-646.
DR PDBsum; 7A9W; -.
DR PDBsum; 7A9X; -.
DR AlphaFoldDB; P53140; -.
DR SMR; P53140; -.
DR BioGRID; 33143; 242.
DR IntAct; P53140; 4.
DR STRING; 4932.YGL107C; -.
DR MaxQB; P53140; -.
DR PaxDb; P53140; -.
DR PRIDE; P53140; -.
DR EnsemblFungi; YGL107C_mRNA; YGL107C; YGL107C.
DR GeneID; 852771; -.
DR KEGG; sce:YGL107C; -.
DR SGD; S000003075; RMD9.
DR VEuPathDB; FungiDB:YGL107C; -.
DR eggNOG; ENOG502QUSW; Eukaryota.
DR GeneTree; ENSGT00940000176413; -.
DR HOGENOM; CLU_019840_0_0_1; -.
DR InParanoid; P53140; -.
DR OMA; HIYELNT; -.
DR BioCyc; YEAST:G3O-30606-MON; -.
DR PRO; PR:P53140; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53140; protein.
DR GO; GO:0031314; C:extrinsic component of mitochondrial inner membrane; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; IDA:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0070935; P:3'-UTR-mediated mRNA stabilization; IDA:UniProtKB.
DR GO; GO:0009060; P:aerobic respiration; IMP:SGD.
DR GO; GO:0043488; P:regulation of mRNA stability; IMP:SGD.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR GO; GO:0006413; P:translational initiation; IGI:SGD.
DR Gene3D; 1.25.40.10; -; 1.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Membrane; Mitochondrion;
KW Mitochondrion inner membrane; Phosphoprotein; Reference proteome; Repeat;
KW RNA-binding; Sporulation; Transit peptide.
FT TRANSIT 1..14
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT PROPEP 15..51
FT /note="Removed in mature form"
FT /evidence="ECO:0000269|PubMed:33876744"
FT /id="PRO_0000454658"
FT CHAIN 52..646
FT /note="RNA-binding protein RMD9, mitochondrial"
FT /id="PRO_0000202752"
FT REPEAT 209..238
FT /note="PPR1"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 251..282
FT /note="PPR2"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 288..317
FT /note="PPR3"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 323..353
FT /note="PPR4"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 363..394
FT /note="PPR5"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 401..439
FT /note="PPR6"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 444..473
FT /note="PPR7"
FT /evidence="ECO:0000305|PubMed:33876744"
FT REPEAT 481..514
FT /note="PPR8"
FT /evidence="ECO:0000305|PubMed:33876744"
FT MUTAGEN 363
FT /note="V->I: Causes respiratory deficiency in absence of
FT RSM28."
FT /evidence="ECO:0000269|PubMed:17194786"
FT CONFLICT 426
FT /note="F -> S (in Ref. 4; AAU09725)"
FT /evidence="ECO:0000305"
FT HELIX 84..102
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 121..140
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 148..171
FT /evidence="ECO:0007829|PDB:7A9X"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 183..204
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 211..223
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 227..236
FT /evidence="ECO:0007829|PDB:7A9X"
FT TURN 237..239
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 243..248
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 252..266
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 270..280
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 288..300
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 304..317
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 320..322
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 324..335
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 340..351
FT /evidence="ECO:0007829|PDB:7A9X"
FT STRAND 355..357
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 363..377
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 380..394
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 400..417
FT /evidence="ECO:0007829|PDB:7A9X"
FT TURN 418..420
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 422..439
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 444..453
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 454..456
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 460..472
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 479..488
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 489..491
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 497..513
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 521..529
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 532..545
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 583..594
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 595..597
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 602..606
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 609..614
FT /evidence="ECO:0007829|PDB:7A9X"
FT HELIX 616..621
FT /evidence="ECO:0007829|PDB:7A9X"
FT TURN 623..627
FT /evidence="ECO:0007829|PDB:7A9W"
SQ SEQUENCE 646 AA; 74596 MW; 8AEB42E9BDD9DC73 CRC64;
MMLRRNAVRS LKTMEISVSN VVNSGSIAML RGKLANVVLS DRTYHSSPIF HKNVPKGVLD
KKNGREQRKT EQNVFNVDPA SPWRHELLSF DECVSSALKY STTPLQNTYK RIGNNQLNKN
PSFAMFWDSM GRAMELYYSL RESPDFNAYR VSRLIHLLHN GLRSTRDQLV KLSRKPDYDS
QSFHKEMMNF LCNSLKDISD DILIGKVSVS GYGATHLLTS FKELSFDDDC IRIWEASKNL
SDETTSQAFQ EPKVVGFMLP LLYAKTRSLT EPNELYNQII QSKEFIHPNL YSGLIKVFIK
AEDYEKALSL FGQLCEKAEV RNYGYLIETH LSFIGDSKNL TLAESFFDKI INDEMPYKII
LQVSTVNSFL QNIWKAQNDF DHVYRIWEKA VKFYGNTVNP GILSSLNNTF FTIFFENYIN
DNINGFRKLQ EIITFYSGVK KIDEPFFNVM LTRASIWHER SIIDFIDKNY TLYHIPRTII
SYRILLKSLG SIDNTNNEEI LDRWLELVKK LNELGQQYIA NADLSALRDA TVVWSQSKRD
EKVFSAKAKG TPATTTTTED DIKVPKPLEN LKNEDSTSNS EDRIELYLKI LKRYTPYFRA
TKQVYRYTTG CAESYPILNE YLSGYSDLSA EDIPVPQLHS FIAKEQ
