Ribosomal protein

Mitochondrial ribosomal protein L31
Identifiers
Symbol L31
Pfam PF09784
InterPro IPR016340
PROSITE PDOC00880
SCOP 1m90
SUPERFAMILY 1m90

A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. A large part of the knowledge about these organic molecules has come from the study of E. coli ribosomes. All ribosomal proteins have been isolated and many specific antibodies have been produced. These, together with electronic microscopy and the use of certain reactives, have allowed for the determination of the topography of the proteins in the ribosome. E.coli, other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit.[1] Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans.[2] More recently, a near-complete (near)atomic picture of the ribosomal proteins is emerging from the latest high-resolution cryo-EM data (including PDB ID: 5AFI).

Proteins in E. coli ribosomes

The ribosome of E. coli has about 22 proteins in the small subunit (labelled S1 to S22) and 33 proteins in the large subunit (somewhat counter-intuitively called L1 to L36). All of them are different with three exceptions: one protein is found in both subunits (S20 and L26), L7 and L12 are acetylated and methylated forms of the same protein, and L8 is a complex of L7/L12 and L10. In addition, L31 is known to exist in two forms, the full length at 7.9 kilodaltons (kDa) and fragmented at 7.0 kDa. This is why the number of proteins in a ribosome is of 56. Except for S1 (with a molecular weight of 61.2 kDa), the other proteins range in weight between 4.4 and 29.7 kDa.[3]

Recent 'de novo' proteomics experiments where the authors characterized in vivo ribosome-assembly intermediates and associated assembly factors from wild-type Escherichia coli cells using a general quantitative mass spectrometry (qMS) approach have confirmed the presence of all the known small and large subunit components and have identified a total of 21 known and potentially new ribosome-assembly-factors that co-localise with various ribosomal particles.[4]

Disposition in the small ribosomal subunit

In the small (30S) subunit of E. coli ribosomes, the proteins denoted S4, S7, S8, S15, S17, S20 bind independently to 16S rRNA. After assembly of these primary binding proteins, S5, S6, S9, S12, S13, S16, S18, and S19 bind to the growing ribosome. These proteins also potentiate the addition of S2, S3, S10, S11, S14, and S21. Protein binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure. Nearly all the proteins contain one or more globular domains. Moreover, nearly all contain long extensions that can contact the RNA in far-reaching regions. Additional stabilization results from the proteins' basic residues, as these neutralize the charge repulsion of the RNA backbone. Protein-protein interactions also exist to hold structure together by electrostatic and hydrogen bonding interactions. Theoretical investigations pointed to correlated effects of protein-binding onto binding affinities during the assembly process [5]

Table of E.coli small 30S ribosomal subunit proteins

Subunit No. Subunit name E.coli protein Pfam family with E.coli protein Uniprot accession of E.coli protein
1 30S ribosomal protein S1 RS1_ECOLI PF00575 P0AG67
2 30S ribosomal protein S2 RS2_ECOLI PF00318 P0A7V0
3 30S ribosomal protein S3 RS3_ECOLI PF00189 ,PF07650 P0A7V3
4 30S ribosomal protein S4 RS4_ECOLI PF00163 ,PF01479 P0A7V8
5 30S ribosomal protein S5 RS5_ECOLI PF00333 ,PF03719 P0A7W1
6 30S ribosomal protein S6 RS6_ECOLI PF01250 P02358
7 30S ribosomal protein S7 RS7_ECOLI PF00177 P02359
8 30S ribosomal protein S8 RS8_ECOLI PF00410 P0A7W7
9 30S ribosomal protein S9 RS9_ECOLI PF00380 P0A7X3
10 30S ribosomal protein S10 RS10_ECOLI PF00338 P0A7R5
11 30S ribosomal protein S11 RS11_ECOLI PF00411 P0A7R9
12 30S ribosomal protein S12 RS12_ECOLI PF00164 P0A7S3
13 30S ribosomal protein S13 RS13_ECOLI PF00416 P0A7S9
14 30S ribosomal protein S14 RS14_ECOLI PF00253 P0AG59
15 30S ribosomal protein S15 RS15_ECOLI PF00312 P0ADZ4
16 30S ribosomal protein S16 RS16_ECOLI PF00886 P0A7T3
27 30S ribosomal protein S17 RS17_ECOLI PF00366 P0AG63
28 30S ribosomal protein S18 RS18_ECOLI PF01084 P0A7T7
29 30S ribosomal protein S19 RS19_ECOLI PF00203 P0A7U3
20 30S ribosomal protein S20 RS20_ECOLI PF01649 P0A7U7
21 30S ribosomal protein S21 RS21_ECOLI PF01165 P68681
22 30S ribosomal protein S22 RS22_ECOLI PF08136 C8U8F3

Assembly of the ribosome in eukaryotes

Ribosomes, which synthesize the proteome of cells, are complex ribonucleoproteins that, in eukaryotes, contain 79–80 proteins and four ribosomal RNAs(rRNAs). General or specialized chaperones solubilize the ribosomal proteins and facilitate their import into the nucleus. Assembly of the eukaryotic ribosome appears to be driven by the ribosomal proteins in vivo when assembly is also aided by chaperones. Most ribosomal proteins assemble with rRNA co-transcriptionally, becoming associated more stably as assembly proceeds, and the active sites of both subunits are constructed last.[2]

Table of E.coli large 50S ribosomal subunit proteins

Subunit No. Subunit name E.coli protein Pfam family with E.coli protein Uniprot accession of E.coli protein
1 50S ribosomal protein L1 RL1_ ECOLI PF00687 Ribosomal protein L1p/L10e family P0A7L0
2 50S ribosomal protein L2 RL2_ ECOLI PF03947 Ribosomal Proteins L2, C-terminal domain P60422
2 50S ribosomal protein L2 RL2_ ECOLI PF00181 Ribosomal Proteins L2, RNA binding domain P60422
3 50S ribosomal protein L3 RL3_ ECOLI PF00297 Ribosomal protein L3 P60438
4 50S ribosomal protein L4 RL4_ ECOLI PF00573 Ribosomal protein L4/L1 family P60723
5 50S ribosomal protein L5 RL5_ ECOLI PF00281 Ribosomal protein L5 P62399
5 50S ribosomal protein L5 RL5_ ECOLI PF00673 ribosomal L5P family C-terminus P62399
6 50S ribosomal protein L6 RL6_ ECOLI PF00347 Ribosomal protein L6 P0AG55
7/12 50S ribosomal protein L7/L12 RL7_ ECOLI PF16320 Ribosomal protein L7/L12 dimerisation domain P0A7K2
8 50S ribosomal protein L7/L12 RL7_ ECOLI PF00542 Ribosomal protein L7/L12 C-terminal domain P0A7K2
9 50S ribosomal protein L9 RL9_ ECOLI PF03948 Ribosomal protein L9, C-terminal domain P0A7R1
9 50S ribosomal protein L9 RL9_ ECOLI PF01281 Ribosomal protein L9, N-terminal domain P0A7R1
10 50S ribosomal protein L10 RL10_ ECOLI PF00466 Ribosomal protein L10 P0A7J3
11 50S ribosomal protein L11 RL11_ ECOLI PF03946 Ribosomal protein L11, N-terminal domain P0A7J7
11 50S ribosomal protein L11 RL11_ ECOLI PF00298 Ribosomal protein L11, RNA binding domain P0A7J7
13 50S ribosomal protein L13 RL13_ ECOLI PF00572 Ribosomal protein L13 P0AA10
14 50S ribosomal protein L14 RL14_ ECOLI PF00238 Ribosomal protein L14p/L23e P0ADY3
15 50S ribosomal protein L15 RL15_ ECOLI PF00828 Ribosomal protein L18e/L15 P02413
16 50S ribosomal protein L16 RL16_ ECOLI PF00252 Ribosomal protein L16p/L10e P0ADY7
17 50S ribosomal protein L17 RL17_ ECOLI PF01196 Ribosomal protein L17 P0AG44
18 50S ribosomal protein L18 RL18_ ECOLI PF00861 Ribosomal L18p/L5e family P0C018
19 50S ribosomal protein L19 RL19_ ECOLI PF01245 Ribosomal protein L19 B1LPB3
20 50S ribosomal protein L20 RL20_ ECOLI PF00453 Ribosomal protein L20 P0A7L3
21 50S ribosomal protein L21 RL21_ ECOLI PF00829 Ribosomal prokaryotic L21 protein P0AG48
22 50S ribosomal protein L22 RL22_ ECOLI PF00237 Ribosomal protein L22p/L17e P61175
23 50S ribosomal protein L23 RL23_ ECOLI PF00276 Ribosomal protein L23 P0ADZ0
24 50S ribosomal protein L24 RL24_ ECOLI PF00467 KOW motif P60624
25 50S ribosomal protein L25 RL25_ ECOLI PF01386 Ribosomal L25p family P68919
27 50S ribosomal protein L27 RL27_ ECOLI PF01016 Ribosomal L27 protein P0A7M0
28 50S ribosomal protein L28 RL28_ ECOLI PF00830 Ribosomal L28 family P0A7M2
29 50S ribosomal protein L29 RL29_ ECOLI PF00831 Ribosomal L29 protein P0A7M6
30 50S ribosomal protein L30 RL30_ ECOLI PF00327 Ribosomal protein L30p/L7e P0AG51
31 50S ribosomal protein L31 RL31_ ECOLI PF01197 Ribosomal protein L31 P0A7M9
31B 50S ribosomal protein L31 type B RL31B_ ECOLI PF01197 Ribosomal protein L31 P0A7M9
32 50S ribosomal protein L32 RL32_ ECOLI PF01783 Ribosomal L32p protein family C4ZS29
33 50S ribosomal protein L33 RL33_ ECOLI PF00471 Ribosomal protein L33 P0A7N9
34 50S ribosomal protein L34 RL34_ ECOLI PF00468 Ribosomal protein L34 P0A7P6
35 50S ribosomal protein L35 RL35_ ECOLI PF01632 Ribosomal protein L35 P0A7Q2
36 50S ribosomal protein L36 RL36_ ECOLI PF00444 Ribosomal protein L36 P0A7Q7

Table of Human small 40S ribosomal subunit proteins

Subunit No. Subunit name Human protein Pfam family with Human protein
2 40S ribosomal protein S2 RS2_HUMAN PF03719 Ribosomal protein S5, C-terminal domain
2 40S ribosomal protein S2 RS2_HUMAN PF00333 Ribosomal protein S5, N-terminal domain
3 40S ribosomal protein S3 RS3_HUMAN PF00189 Ribosomal protein S3, C-terminal domain
3A 40S ribosomal protein S3a RS3A_HUMAN PF01015 Ribosomal S3Ae family
4 40S ribosomal protein S4, X isoform RS4X_HUMAN PF08071 RS4NT (NUC023) domain
4 40S ribosomal protein S4, X isoform RS4X_HUMAN PF01479 S4 domain
4 40S ribosomal protein S4, X isoform RS4X_HUMAN PF00900 Ribosomal family S4e
4 40S ribosomal protein S4, X isoform RS4X_HUMAN PF16121 40S ribosomal protein S4 C-terminus
4 40S ribosomal protein S4, Y isoform 1 RS4Y1_HUMAN PF08071 RS4NT (NUC023) domain
4 40S ribosomal protein S4, Y isoform 1 RS4Y1_HUMAN PF00900 Ribosomal family S4e
4 40S ribosomal protein S4, Y isoform 1 RS4Y1_HUMAN PF16121 40S ribosomal protein S4 C-terminus
4 40S ribosomal protein S4, Y isoform 2 RS4Y2_HUMAN PF08071 RS4NT (NUC023) domain
4 40S ribosomal protein S4, Y isoform 2 RS4Y2_HUMAN PF00900 Ribosomal family S4e
4 40S ribosomal protein S4, Y isoform 2 RS4Y2_HUMAN PF16121 40S ribosomal protein S4 C-terminus
5 40S ribosomal protein S5 RS5_HUMAN PF00177 Ribosomal protein S7p/S5e
6 40S ribosomal protein S6 RS6_HUMAN PF01092 Ribosomal protein S6e
7 40S ribosomal protein S7 RS7_HUMAN PF01251 Ribosomal protein S7e
8 40S ribosomal protein S8 RS8_HUMAN PF01201 Ribosomal protein S8e
9 40S ribosomal protein S9 RS9_HUMAN PF01479 S4 domain
9 40S ribosomal protein S9 RS9_HUMAN PF00163 Ribosomal protein S4/S9 N-terminal domain
10 40S ribosomal protein S10 RS10_HUMAN PF03501 Plectin/S10 domain
11 40S ribosomal protein S11 RS11_HUMAN PF16205 Ribosomal_S17 N-terminal
11 40S ribosomal protein S11 RS11_HUMAN PF00366 Ribosomal protein S17
12 40S ribosomal protein S12 RS12_HUMAN PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
13 40S ribosomal protein S13 RS13_HUMAN PF08069 Ribosomal S13/S15 N-terminal domain
13 40S ribosomal protein S13 RS13_HUMAN PF00312 Ribosomal protein S15
14 40S ribosomal protein S14 RS14_HUMAN PF00411 Ribosomal protein S11
15 40S ribosomal protein S15 RS15_HUMAN PF00203 Ribosomal protein S19
15A 40S ribosomal protein S15a RS15A_HUMAN PF00410 Ribosomal protein S8
16 40S ribosomal protein S16 RS16_HUMAN PF00380 Ribosomal protein S9/S16
17 40S ribosomal protein S17 RS17_HUMAN PF00833 Ribosomal S17
18 40S ribosomal protein S18 RS18_HUMAN PF00416 Ribosomal protein S13/S18
19 40S ribosomal protein S19 RS19_HUMAN PF01090 Ribosomal protein S19e
20 40S ribosomal protein S20 RS20_HUMAN PF00338 Ribosomal protein S10p/S20e
21 40S ribosomal protein S21 RS21_HUMAN PF01249 Ribosomal protein S21e
23 40S ribosomal protein S23 RS23_HUMAN PF00164 Ribosomal protein S12/S23
24 40S ribosomal protein S24 RS24_HUMAN PF01282 Ribosomal protein S24e
25 40S ribosomal protein S25 RS25_HUMAN PF03297 S25 ribosomal protein
26 40S ribosomal protein S26 RS26_HUMAN PF01283 Ribosomal protein S26e
27 40S ribosomal protein S27 RS27_HUMAN PF01667 Ribosomal protein S27
28 40S ribosomal protein S28 RS28_HUMAN PF01200 Ribosomal protein S28e
29 40S ribosomal protein S29 RS29_HUMAN PF00253 Ribosomal protein S14p/S29e
30 40S ribosomal protein S30 RS30_HUMAN PF04758 Ribosomal protein S30
A 40S ribosomal protein SA RSSA_HUMAN PF16122 40S ribosomal protein SA C-terminus
A 40S ribosomal protein SA RSSA_HUMAN PF00318 Ribosomal protein S2

Table of Human large 60S ribosomal subunit proteins

Subunit No. Subunit name Human protein Pfam family with Human protein
3 60S ribosomal protein L3 RL3_HUMAN PF00297 Ribosomal protein L3
4 60S ribosomal protein L4 RL4_HUMAN PF00573 Ribosomal protein L4/L1 family
4 60S ribosomal protein L4 RL4_HUMAN PF14374 60S ribosomal protein L4
5 60S ribosomal protein L5 RL5_HUMAN PF00861 Ribosomal L18p/L5e family
5 60S ribosomal protein L5 RL5_HUMAN PF14204 Ribosomal L18 C-terminal region
6 60S ribosomal protein L6 RL6_HUMAN PF01159 Ribosomal protein L6e
6 60S ribosomal protein L6 RL6_HUMAN PF03868 Ribosomal protein L6, N-terminal
7A 60S ribosomal protein L7a RL7A_HUMAN PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
7 60S ribosomal protein L7 RL7_HUMAN PF00327 Ribosomal protein L30p/L7e
7 60S ribosomal protein L7 RL7_HUMAN PF08079 Ribosomal L30 N-terminal domain
8 60S ribosomal protein L8 RL8_HUMAN PF00181 Ribosomal Proteins L2, RNA-binding domain
8 60S ribosomal protein L8 RL8_HUMAN PF03947 Ribosomal Proteins L2, C-terminal
9 60S ribosomal protein L9 RL9_HUMAN PF00347 Ribosomal protein L6
9 60S ribosomal protein L9 RL9_HUMAN PF00347 Ribosomal protein L6
10A 60S ribosomal protein L10a RL10A_HUMAN PF00687 Ribosomal protein L1p/L10e family
10 60S ribosomal protein L10 RL10_HUMAN PF00252 Ribosomal protein L16p/L10e
11 60S ribosomal protein L11 RL11_HUMAN PF00281 Ribosomal protein L5
11 60S ribosomal protein L11 RL11_HUMAN PF00673 ribosomal L5P family C-terminus
12 60S ribosomal protein L12 RL12_HUMAN PF00298 Ribosomal protein L11, RNA-binding domain
12 60S ribosomal protein L12 RL12_HUMAN PF03946 Ribosomal protein L11, N-terminal
13A 60S ribosomal protein L13a RL13A_HUMAN PF00572 Ribosomal protein L13
13 60S ribosomal protein L13 RL13_HUMAN PF01294 Ribosomal protein L13e
14 60S ribosomal protein L14 RL14_HUMAN PF01929 Ribosomal protein L14
15 60S ribosomal protein L15 RL15_HUMAN PF00827 Ribosomal L15
17 60S ribosomal protein L17 RL17_HUMAN PF00237 Ribosomal protein L22p/L17e
18A 60S ribosomal protein L18a RL18A_HUMAN PF01775 Ribosomal L18ae/LX protein domain
18 60S ribosomal protein L18 RL18_HUMAN PF00828 Ribosomal_L18e
19 60S ribosomal protein L19 RL19_HUMAN PF01280 Ribosomal protein L19e
21 60S ribosomal protein L21 RL21_HUMAN PF01157 Ribosomal protein L21e
22 60S ribosomal protein L22 RL22_HUMAN PF01776 Ribosomal L22e protein family
23A 60S ribosomal protein L23a RL23A_HUMAN PF00276 Ribosomal protein L23
23A 60S ribosomal protein L23a RL23A_HUMAN PF03939 Ribosomal protein L23, N-terminal
23 60S ribosomal protein L23 RL23_HUMAN PF00238 Ribosomal protein L14p/L23e
24 60S ribosomal protein L24 RL24_HUMAN PF01246 Ribosomal protein L24e
26 60S ribosomal protein L26 RL26_HUMAN PF16906 Ribosomal proteins L26 eukaryotic, L24P archaeal
27A 60S ribosomal protein L27a RL27A_HUMAN PF00828 Ribosomal protein L18e/L15
27 60S ribosomal protein L27 RL27_HUMAN PF01777 Ribosomal L27e protein family
28 60S ribosomal protein L28 RL28_HUMAN PF01778 Ribosomal L28e protein family
29 60S ribosomal protein L29 RL29_HUMAN PF01779 Ribosomal L29e protein family
30 60S ribosomal protein L30 RL30_HUMAN PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
31 60S ribosomal protein L31 RL31_HUMAN PF01198 Ribosomal protein L31e
32 60S ribosomal protein L32 RL32_HUMAN PF01655 Ribosomal protein L32
34 60S ribosomal protein L34 RL34_HUMAN PF01199 Ribosomal protein L34e
35A 60S ribosomal protein L35a RL35A_HUMAN PF01247 Ribosomal protein L35Ae
35 60S ribosomal protein L35 RL35_HUMAN PF00831 Ribosomal L29 protein
36A 60S ribosomal protein L36a RL36A_HUMAN PF00935 Ribosomal protein L44
34 60S ribosomal protein L36 RL36_HUMAN PF01158 Ribosomal protein L36e
37A 60S ribosomal protein L37a RL37A_HUMAN PF01780 Ribosomal L37ae protein family
37 60S ribosomal protein L37 RL37_HUMAN PF01907 Ribosomal protein L37e
38 60S ribosomal protein L38 RL38_HUMAN PF01781 Ribosomal L38e protein family
39 60S ribosomal protein L39 RL39_HUMAN PF00832 Ribosomal L39 proteiin
40 Ubiquitin-60S ribosomal protein L40 RL40_HUMAN PF01020 Ribosomal L40e family
41 60S ribosomal protein L41 RL41_HUMAN PF05162 Ribosomal protein L41
P0 60S acidic ribosomal protein P0 RLA0_HUMAN PF00466 Ribosomal protein L10
P0 60S acidic ribosomal protein P0 RLA0_HUMAN PF00428 60s Acidic ribosomal protein
P1 60S acidic ribosomal protein P1 RLA1_HUMAN PF00428 60s Acidic ribosomal protein
P1 60S acidic ribosomal protein P2 RLA2_HUMAN PF00428 60s Acidic ribosomal protein

See also

References

  1. ↑ Rodnina MV, Wintermeyer W (Apr 2011). "The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation". Biochemical Society Transactions 39 (2): 658–62. doi:10.1042/BST0390658. PMID 21428957.
  2. 1 2 Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, Lafontaine DL, Lindahl L, Liljas A, Lipton JM, McAlear MA, Moore PB, Noller HF, Ortega J, Panse VG, Ramakrishnan V, Spahn CM, Steitz TA, Tchorzewski M, Tollervey D, Warren AJ, Williamson JR, Wilson D, Yonath A, Yusupov M (Feb 2014). "A new system for naming ribosomal proteins". Current Opinion in Structural Biology 24: 165–9. doi:10.1016/j.sbi.2014.01.002. PMC 4358319. PMID 24524803.
  3. ↑ Arnold RJ, Reilly JP (Apr 1999). "Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry". Analytical Biochemistry 269 (1): 105–12. doi:10.1006/abio.1998.3077. PMID 10094780.
  4. ↑ Chen SS, Williamson JR (Feb 2013). "Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry". Journal of Molecular Biology 425 (4): 767–79. doi:10.1016/j.jmb.2012.11.040. PMC 3568210. PMID 23228329.
  5. ↑ Hamacher K, Trylska J, McCammon JA (Feb 2006). "Dependency map of proteins in the small ribosomal subunit". PLoS Computational Biology 2 (2): e10. doi:10.1371/journal.pcbi.0020010. PMC 1364506. PMID 16485038.

Further reading

External links

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