Reviewed, UniProtKB/Swiss-Prot P17079 (RL12_YEAST)

Names and origin

Protein names

Recommended name:
    60S ribosomal protein L12
Alternative name(s):
    L15
    YL23

Gene names

Name:	RPL12A
Synonyms:	RPL15B
Ordered Locus Names:	YEL054C
AND
Name:	RPL12B
Synonyms:	RPL15A
Ordered Locus Names:	YDR418W
ORF Names:	D9461.7

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	165 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	This protein binds directly to 26S ribosomal RNA.
Subunit structure	Component of the large ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains 32 different proteins (encoded by 56 genes) and 1 molecule of RNA (18S). The 60S subunit contains 46 different proteins (encoded by 81 genes) and 3 molecules of RNA (25S, 5.8S and 5S). Ref.7
Subcellular location	Cytoplasm.
Post-translational modification	It appears that the main modified species for L12 contains 6 methyl groups, 2 on Pro-2, 3 on Lys-4 and 1 on Arg-67. Although not reproduced with a second method, methylation at Lys-11 cannot be ruled out.
Miscellaneous	Present with 118800 molecules/cell in log phase SD medium. Ref.12 There are 2 genes for L12 in yeast.
Sequence similarities	Belongs to the ribosomal protein L11P family.
Mass spectrometry	Molecular mass is 17764.712 Da from positions 2 - 106. Determined by ESI. Monoisotopic mass with 6 methylation modifications. Ref.10

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	RNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Methylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	ribosomal large subunit assembly Inferred from mutant phenotype. Source: SGD translation Ref.7 Traceable author statement. Source: SGD
Cellular component	cytosolic large ribosomal subunit Ref.7 Traceable author statement. Source: SGD
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW structural constituent of ribosome Ref.7 Traceable author statement. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed Ref.5
	Chain	2 – 165	164	60S ribosomal protein L12		PRO_0000104467
Amino acid modifications
	Modified residue	2	1	N,N-dimethylproline Ref.18
	Modified residue	4	1	N6,N6,N6-trimethyllysine; by RKM2 Ref.5 Ref.18
	Modified residue	11	1	N6,N6,N6-trimethyllysine; by RKM2 Ref.5
	Modified residue	38	1	Phosphoserine Ref.9 Ref.13 Ref.14 Ref.15
	Modified residue	67	1	N5-methylarginine; by RMT2 Ref.18 Ref.8
	Modified residue	78	1	Phosphoserine Ref.15
Experimental info
	Mutagenesis	67	1	R → K: Abolishes monomethylation by RMT2. Ref.8

Sequences

	Sequence		Length	Mass (Da)
	P17079-1 [UniParc]. Last modified August 1, 1990. Version 1. Checksum: 0B23A483781DFBE5	FASTA	165	17,823
	10 20 30 40 50 60 MPPKFDPNEV KYLYLRAVGG EVGASAALAP KIGPLGLSPK KVGEDIAKAT KEFKGIKVTV 70 80 90 100 110 120 QLKIQNRQAA ASVVPSASSL VITALKEPPR DRKKDKNVKH SGNIQLDEII EIARQMRDKS 130 140 150 160 FGRTLASVTK EILGTAQSVG CRVDFKNPHD IIEGINAGEI EIPEN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The 26S rRNA binding ribosomal protein equivalent to bacterial protein L11 is encoded by unspliced duplicated genes in Saccharomyces cerevisiae." Pucciarelli G., Remacha M., Ballesta J.P.G. Nucleic Acids Res. 18:4409-4416(1990) [PubMed: 2167467] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (RPL12A AND RPL12B). Strain: Y166.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed: 9169868] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (RPL12A). Strain: ATCC 204511 / S288c / AB972.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (RPL12B). Strain: ATCC 204508 / S288c.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"A novel SET domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10." Porras-Yakushi T.R., Whitelegge J.P., Clarke S. J. Biol. Chem. 281:35835-35845(2006) [PubMed: 17005568] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-16, METHYLATION AT LYS-4 AND LYS-11, MASS SPECTROMETRY.
[6]	"Yeast ribosomal proteins. VIII. Isolation of two proteins and sequence characterization of twenty-four proteins from cytoplasmic ribosomes." Otaka E., Higo K., Itoh T. Mol. Gen. Genet. 195:544-546(1984) Cited for: PROTEIN SEQUENCE OF 17-36.
[7]	"The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae." Planta R.J., Mager W.H. Yeast 14:471-477(1998) [PubMed: 9559554] [Abstract] Cited for: NOMENCLATURE, SUBUNIT.
[8]	"Yeast ribosomal protein L12 is a substrate of protein-arginine methyltransferase 2." Chern M.-K., Chang K.-N., Liu L.-F., Tam T.-C.S., Liu Y.-C., Liang Y.-L., Tam M.F. J. Biol. Chem. 277:15345-15353(2002) [PubMed: 11856739] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, METHYLATION AT ARG-67, MUTAGENESIS OF ARG-67.
[9]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed: 11875433] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38, MASS SPECTROMETRY.
[10]	"Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR." Lee S.-W., Berger S.J., Martinovic S., Pasa-Tolic L., Anderson G.A., Shen Y., Zhao R., Smith R.D. Proc. Natl. Acad. Sci. U.S.A. 99:5942-5947(2002) [PubMed: 11983894] [Abstract] Cited for: MASS SPECTROMETRY.
[11]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[12]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[13]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38, MASS SPECTROMETRY.
[14]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38, MASS SPECTROMETRY.
[15]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38 AND SER-78, MASS SPECTROMETRY.
[16]	"Structure of the 80S ribosome from Saccharomyces cerevisiae -- tRNA-ribosome and subunit-subunit interactions." Spahn C.M.T., Beckmann R., Eswar N., Penczek P.A., Sali A., Blobel G., Frank J. Cell 107:373-386(2001) [PubMed: 11701127] [Abstract] Cited for: 3D-STRUCTURE MODELING OF 13-143, ELECTRON MICROSCOPY.
[17]	"Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation." Spahn C.M.T., Gomez-Lorenzo M.G., Grassucci R.A., Joergensen R., Andersen G.R., Beckmann R., Penczek P.A., Ballesta J.P.G., Frank J. EMBO J. 23:1008-1019(2004) [PubMed: 14976550] [Abstract] Cited for: 3D-STRUCTURE MODELING OF 13-143, ELECTRON MICROSCOPY.
[18]	"Identification of two SET domain proteins required for methylation of lysine residues in yeast ribosomal protein Rpl42ab." Webb K.J., Laganowsky A., Whitelegge J.P., Clarke S.G. J. Biol. Chem. 283:35561-35568(2008) [PubMed: 18957409] [Abstract] Cited for: METHYLATION AT PRO-2; LYS-4 AND ARG-67.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X51519 Genomic DNA. Translation: CAA35891.1.
X51520 Genomic DNA. Translation: CAA35892.1.
U18795 Genomic DNA. Translation: AAB65033.1.
U33007 Genomic DNA. Translation: AAB64852.1.
AY693201 Genomic DNA. Translation: AAT93220.1.

PIR

S13665.

RefSeq

NP_010706.1.
NP_010860.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K5Y	model	-	K	13-143	[»]
1S1I	electron microscopy	11.70	K	13-143	[»]

SMR

P17079. Positions 2-80.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2505N.

IntAct

P17079. 46 interactions.

STRING

P17079.

Proteomic databases

PRIDE

P17079.

Genome annotation databases

Ensembl

YDR418W; YDR418W; YDR418W; Saccharomyces cerevisiae. [Genome view]
YEL054C; YEL054C; YEL054C; Saccharomyces cerevisiae. [Genome view]

GeneID

852026.
856656.

KEGG

sce:YDR418W.
sce:YEL054C.

Organism-specific databases

CYGD

YDR418w.
YEL054c.

SGD

S000000780. RPL12A.
S000002826. RPL12B.

Phylogenomic databases

HOGENOM

P17079.

OMA

IQNRQAT

OrthoDB

EOG93XWKK

Gene expression databases

ArrayExpress

P17079.

Genevestigator

P17079.

GermOnline

YDR418W. Saccharomyces cerevisiae.
YEL054C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000911. Ribosomal_L11.
IPR020783. Ribosomal_L11_C.
IPR020785. Ribosomal_L11_CS.
IPR020784. Ribosomal_L11_N.
[Graphical view]

Gene3D

G3DSA:3.30.1550.10. Ribosomal_L11_N. 1 hit.

PANTHER

PTHR11661. Ribosomal_L11. 1 hit.

Pfam

PF00298. Ribosomal_L11. 1 hit.
PF03946. Ribosomal_L11_N. 1 hit.
[Graphical view]

SMART

SM00649. RL11. 1 hit.
[Graphical view]

PROSITE

PS00359. RIBOSOMAL_L11. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

970252.

Entry information

Entry name

RL12_YEAST

Accession

Primary (citable) accession number: P17079
Secondary accession number(s): P05741

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	August 1, 1990
Last modified:	November 24, 2009
This is version 102 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)