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MetaCyc Polypeptide: 50S ribosomal subunit protein L13

Gene: rplM Accession Numbers: EG10874 (MetaCyc), b3231, ECK3220

Species: Escherichia coli K-12 substr. MG1655

Component of:
50S ribosomal subunit
ribosome

Summary:
The L13 protein is an early assembly component of the 50S subunit of the ribosome. The RNA helicase SrmB is necessary for the assembly of L13 into the ribosome [Charollais03].

L13 interacts with 23S rRNA [Spierer75, Spierer76, Skold81, Osswald90, Tumminia94] and crosslinks to it in both free ribosomes and the initiation complex [Chistyakov89]. L13 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center [Muralikrishna95]. L13 binds to 5S rRNA [Kargel87] and can be crosslinked to L2 [Barritault75], L3 [Walleczek89], L20 [Barritault75, Redl89, Walleczek89] and L21 [Schonfeld87, Walleczek89a, Walleczek89]. L13 interacts with tRNA in the P site [Graifer89].

Ribosome modulation factor binds near L2, L13, and S13 [Yoshida02]. A puromycin analog [Krassnigg78], a tobramycin analog [Tangy83], and a pactamycin analog [Tejedor85] can be crosslinked to L13.

L13 has RNA chaperone-like activity in an in vitro trans splicing assay [Semrad04] and binds zinc [Katayama02].

Locations: cytosol, ribosome

Map Position: [3,376,245 <- 3,376,673]

Unification Links: ASAP:ABE-0010599 , CGSC:253 , DIP:DIP-47837N , EchoBASE:EB0867 , EcoGene:EG10874 , EcoliWiki:b3231 , Mint:MINT-1269598 , ModBase:P0AA10 , OU-Microarray:b3231 , PortEco:b3231 , PR:PRO_000023819 , Pride:P0AA10 , Protein Model Portal:P0AA10 , RefSeq:NP_417698 , RegulonDB:EG10874 , SMR:P0AA10 , String:511145.b3231 , UniProt:P0AA10

Relationship Links: InterPro:IN-FAMILY:IPR005822 , InterPro:IN-FAMILY:IPR005823 , InterPro:IN-FAMILY:IPR023563 , InterPro:IN-FAMILY:IPR023564 , Panther:IN-FAMILY:PTHR11545 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00572 , Prosite:IN-FAMILY:PS00783

Ortholog Links: Ecol199310Cyc (Escherichia coli CFT073):C3985 , EcoO157Cyc (Escherichia coli O157:H7 str. EDL933):RPLM , ShigellaCyc (Shigella flexneri 2a str. 2457T):RPLM

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Katayama02]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Credits:
Last-Curated ? 21-Apr-2006 by Keseler I , SRI International


Subunit of: 50S ribosomal subunit

Synonyms: ribosome, large subunit

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of 50S ribosomal subunit = [RplA][RplB][RplC][RplD][RplE][RplF][(RplJ)([RplL]2)2][RplI][RplJ][RplK][RplM][RplN][RplO][RplP][RplQ][RplR][RplS][RplT][RplU][RplV][RplW][RplX][RplY][RpmA][RpmB][RpmC][RpmD][RpmE][RpmF][RpmG][RpmH][RpmI][RpmJ][5S ribosomal RNA (rrfA)][23S ribosomal RNA (rrlA)]
         50S ribosomal subunit protein L1 = RplA (extended summary available)
         50S ribosomal subunit protein L2 = RplB (summary available)
         50S ribosomal subunit protein L3 = RplC (summary available)
         50S ribosomal subunit protein L4 = RplD (extended summary available)
         50S ribosomal subunit protein L5 = RplE (summary available)
         50S ribosomal subunit protein L6 = RplF (summary available)
         50S ribosomal protein complex L8 = (RplJ)([RplL]2)2
                 50S ribosomal subunit protein L10 = RplJ (extended summary available)
                 50S ribosomal subunit protein L7/L12 dimer = (RplL)2
                         50S ribosomal subunit protein L12 = RplL
         50S ribosomal subunit protein L9 = RplI (summary available)
         50S ribosomal subunit protein L10 = RplJ (extended summary available)
         50S ribosomal subunit protein L11 = RplK (extended summary available)
         50S ribosomal subunit protein L13 = RplM (extended summary available)
         50S ribosomal subunit protein L14 = RplN (extended summary available)
         50S ribosomal subunit protein L15 = RplO (summary available)
         50S ribosomal subunit protein L16 = RplP (extended summary available)
         50S ribosomal subunit protein L17 = RplQ (summary available)
         50S ribosomal subunit protein L18 = RplR (extended summary available)
         50S ribosomal subunit protein L19 = RplS (extended summary available)
         50S ribosomal subunit protein L20 = RplT (extended summary available)
         50S ribosomal subunit protein L21 = RplU (summary available)
         50S ribosomal subunit protein L22 = RplV (extended summary available)
         50S ribosomal subunit protein L23 = RplW (extended summary available)
         50S ribosomal subunit protein L24 = RplX (summary available)
         50S ribosomal subunit protein L25 = RplY (summary available)
         50S ribosomal subunit protein L27 = RpmA (extended summary available)
         50S ribosomal subunit protein L28 = RpmB (summary available)
         50S ribosomal subunit protein L29 = RpmC (summary available)
         50S ribosomal subunit protein L30 = RpmD (summary available)
         50S ribosomal subunit protein L31 = RpmE (summary available)
         50S ribosomal subunit protein L32 = RpmF (summary available)
         50S ribosomal subunit protein L33 = RpmG (summary available)
         50S ribosomal subunit protein L34 = RpmH (summary available)
         50S ribosomal subunit protein L35 = RpmI (summary available)
         50S ribosomal subunit protein L36 = RpmJ (summary available)

Component of: ribosome

Credits:
Created 02-Jun-2006 by Keseler I , SRI International


Subunit of: ribosome

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of ribosome = [(RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra)(16S ribosomal RNA (rrsA))][(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplJ)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)(5S ribosomal RNA (rrfA))(23S ribosomal RNA (rrlA))]
         30S ribosomal subunit = (RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra)(16S ribosomal RNA (rrsA))
                 30S ribosomal subunit protein S1 = RpsA (extended summary available)
                 30S ribosomal subunit protein S2 = RpsB (summary available)
                 30S ribosomal subunit protein S3 = RpsC (summary available)
                 30S ribosomal subunit protein S4 = RpsD (extended summary available)
                 30S ribosomal subunit protein S5 = RpsE (extended summary available)
                 30S ribosomal subunit protein S6 = RpsF (extended summary available)
                 30S ribosomal subunit protein S7 = RpsG (extended summary available)
                 30S ribosomal subunit protein S8 = RpsH (extended summary available)
                 30S ribosomal subunit protein S9 = RpsI (extended summary available)
                 30S ribosomal subunit protein S10 = RpsJ (extended summary available)
                 30S ribosomal subunit protein S11 = RpsK (summary available)
                 30S ribosomal subunit protein S12 = RpsL (extended summary available)
                 30S ribosomal subunit protein S13 = RpsM (extended summary available)
                 30S ribosomal subunit protein S14 = RpsN (summary available)
                 30S ribosomal subunit protein S15 = RpsO (extended summary available)
                 30S ribosomal subunit protein S16 = RpsP (summary available)
                 30S ribosomal subunit protein S17 = RpsQ (summary available)
                 30S ribosomal subunit protein S18 = RpsR (extended summary available)
                 30S ribosomal subunit protein S19 = RpsS (summary available)
                 30S ribosomal subunit protein S20 = RpsT (extended summary available)
                 30S ribosomal subunit protein S21 = RpsU (summary available)
                 30S ribosomal subunit protein S22 = Sra (summary available)
         50S ribosomal subunit = (RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplJ)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)(5S ribosomal RNA (rrfA))(23S ribosomal RNA (rrlA))
                 50S ribosomal subunit protein L1 = RplA (extended summary available)
                 50S ribosomal subunit protein L2 = RplB (summary available)
                 50S ribosomal subunit protein L3 = RplC (summary available)
                 50S ribosomal subunit protein L4 = RplD (extended summary available)
                 50S ribosomal subunit protein L5 = RplE (summary available)
                 50S ribosomal subunit protein L6 = RplF (summary available)
                 50S ribosomal protein complex L8 = (RplJ)([RplL]2)2
                         50S ribosomal subunit protein L10 = RplJ (extended summary available)
                         50S ribosomal subunit protein L7/L12 dimer = (RplL)2
                                 50S ribosomal subunit protein L12 = RplL
                 50S ribosomal subunit protein L9 = RplI (summary available)
                 50S ribosomal subunit protein L10 = RplJ (extended summary available)
                 50S ribosomal subunit protein L11 = RplK (extended summary available)
                 50S ribosomal subunit protein L13 = RplM (extended summary available)
                 50S ribosomal subunit protein L14 = RplN (extended summary available)
                 50S ribosomal subunit protein L15 = RplO (summary available)
                 50S ribosomal subunit protein L16 = RplP (extended summary available)
                 50S ribosomal subunit protein L17 = RplQ (summary available)
                 50S ribosomal subunit protein L18 = RplR (extended summary available)
                 50S ribosomal subunit protein L19 = RplS (extended summary available)
                 50S ribosomal subunit protein L20 = RplT (extended summary available)
                 50S ribosomal subunit protein L21 = RplU (summary available)
                 50S ribosomal subunit protein L22 = RplV (extended summary available)
                 50S ribosomal subunit protein L23 = RplW (extended summary available)
                 50S ribosomal subunit protein L24 = RplX (summary available)
                 50S ribosomal subunit protein L25 = RplY (summary available)
                 50S ribosomal subunit protein L27 = RpmA (extended summary available)
                 50S ribosomal subunit protein L28 = RpmB (summary available)
                 50S ribosomal subunit protein L29 = RpmC (summary available)
                 50S ribosomal subunit protein L30 = RpmD (summary available)
                 50S ribosomal subunit protein L31 = RpmE (summary available)
                 50S ribosomal subunit protein L32 = RpmF (summary available)
                 50S ribosomal subunit protein L33 = RpmG (summary available)
                 50S ribosomal subunit protein L34 = RpmH (summary available)
                 50S ribosomal subunit protein L35 = RpmI (summary available)
                 50S ribosomal subunit protein L36 = RpmJ (summary available)

Credits:
Created 15-Jun-2006 by Keseler I , SRI International

History:
10/20/97 Gene b3231 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10874; confirmed by SwissProt match.


References

Barritault75: Barritault D, Expert-Bezancon A, Milet M (1975). "[Nearest-neighbor relationships among 50S ribosomal proteins of E. coli]." C R Acad Sci Hebd Seances Acad Sci D 281(14);1043-6. PMID: 813873

Charollais03: Charollais J, Pflieger D, Vinh J, Dreyfus M, Iost I (2003). "The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli." Mol Microbiol 48(5);1253-65. PMID: 12787353

Chistyakov89: Chistyakov PG, Venjaminova AG, Vladimirov SN, Graifer DM, Kazakov SA, Karpova GG (1989). "Differences in 23 S rRNA-protein neighbourhood in Escherichia coli 70 S ribosomes and 70 S initiation complex. Probing by bifunctional Pt(II)-containing reagent." FEBS Lett 246(1-2);197-201. PMID: 2495985

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Graifer89: Graifer DM, Babkina GT, Matasova NB, Vladimirov SN, Karpova GG, Vlassov VV (1989). "Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives." Biochim Biophys Acta 1008(2);146-56. PMID: 2660905

Hindennach71: Hindennach I, Kaltschmidt E, Wittmann HG (1971). "Ribosomal proteins. Isolation of proteins from 50S ribosomal subunits of Escherichia coli." Eur J Biochem 23(1);12-6. PMID: 4942547

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Kargel87: Kargel HJ, Stahl J, Gross B, Knespel S, Bielka H, Saarma M (1987). "Studies on interaction of 5 S RNA with ribosomal proteins." FEBS Lett 220(1);126-8. PMID: 3301408

Katayama02: Katayama A, Tsujii A, Wada A, Nishino T, Ishihama A (2002). "Systematic search for zinc-binding proteins in Escherichia coli." Eur J Biochem 269(9);2403-13. PMID: 11985624

Krassnigg78: Krassnigg F, Erdmann VA, Fasold H (1978). "The synthesis of a photoreactive puromycin analogue and its application for labeling proteins in the 50-S subunit of Escherichia coli ribosomes." Eur J Biochem 87(3);439-43. PMID: 354931

Muralikrishna95: Muralikrishna P, Cooperman BS (1995). "Ribosomal components neighboring the 2475 loop in Escherichia coli 50S subunits." Biochemistry 34(1);115-21. PMID: 7529559

Osswald90: Osswald M, Greuer B, Brimacombe R (1990). "Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents." Nucleic Acids Res 18(23);6755-60. PMID: 1702198

Redl89: Redl B, Walleczek J, Stoffler-Meilicke M, Stoffler G (1989). "Immunoblotting analysis of protein-protein crosslinks within the 50S ribosomal subunit of Escherichia coli. A study using dimethylsuberimidate as crosslinking reagent." Eur J Biochem 181(2);351-6. PMID: 2653827

Schonfeld87: Schonfeld HJ, Foulaki K (1987). "Preoperative isolation of a reversible protein-protein crosslink generated in 50 S subunits of Escherichia coli ribosomes and identification of its components." Anal Biochem 164(1);23-30. PMID: 3314578

Semrad04: Semrad K, Green R, Schroeder R (2004). "RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli." RNA 10(12);1855-60. PMID: 15525706

Skold81: Skold SE (1981). "RNA-protein complexes identified by crosslinking of polysomes." Biochimie 63(1);53-60. PMID: 6163479

Spierer75: Spierer P, Zimmerman RA, Mackie GA (1975). "RNA-protein interactions in the ribosome. Binding of 50-S-subunit proteins to 5' and 3' terminal segments of the 23-S RNA." Eur J Biochem 52(3);459-68. PMID: 800986

Spierer76: Spierer P, Zimmermann RA (1976). "RNA-protein interactions in the ribosome. Binding of proteins L1, L3, L6, L13 and L23 to specific fragments of the 23S RNA." FEBS Lett 68(1);71-5. PMID: 823048

Tangy83: Tangy F, Capmau ML, Le Goffic F (1983). "Photo-induced labelling of Escherichia coli ribosomes by a tobramycin analog." Eur J Biochem 131(3);581-7. PMID: 6341055

Tejedor85: Tejedor F, Amils R, Ballesta JP (1985). "Photoaffinity labeling of the pactamycin binding site on eubacterial ribosomes." Biochemistry 24(14);3667-72. PMID: 3899171

Tumminia94: Tumminia SJ, Hellmann W, Wall JS, Boublik M (1994). "Visualization of protein-nucleic acid interactions involved in the in vitro assembly of the Escherichia coli 50 S ribosomal subunit." J Mol Biol 235(4);1239-50. PMID: 8308887

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Walleczek89: Walleczek J, Martin T, Redl B, Stoffler-Meilicke M, Stoffler G (1989). "Comparative cross-linking study on the 50S ribosomal subunit from Escherichia coli." Biochemistry 28(9);4099-105. PMID: 2665813

Walleczek89a: Walleczek J, Redl B, Stoffler-Meilicke M, Stoffler G (1989). "Protein-protein cross-linking of the 50 S ribosomal subunit of Escherichia coli using 2-iminothiolane. Identification of cross-links by immunoblotting techniques." J Biol Chem 264(7);4231-7. PMID: 2645289

Yoshida02: Yoshida H, Maki Y, Kato H, Fujisawa H, Izutsu K, Wada C, Wada A (2002). "The ribosome modulation factor (RMF) binding site on the 100S ribosome of Escherichia coli." J Biochem 132(6);983-9. PMID: 12473202

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, BIOCYC13A.