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Ribosomal protein

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Mitochondrial ribosomal protein L31
Identifiers
SymbolL31
PfamPF09784
InterProIPR016340
PROSITEPDOC00880
SCOP21m90 / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

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. Most ribosomal proteins have been isolated and 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]

Proteins in E. coli ribosomes

The ribosome of E. coli has about 22 proteins in the small subunit (labelled S1 to S22) and 34 proteins in the large subunit (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]

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 [4]

Table of E.coli 30S small Ribosomal subunit components

Subunit No. Subunit name E.coli protein Pfam family with E.coli protein
1 30S ribosomal protein S1 RS1_ECOLI PF00575
2 30S ribosomal protein S2 RS2_ECOLI PF00318
3 30S ribosomal protein S3 RS3_ECOLI PF00189 ,PF07650
4 30S ribosomal protein S4 RS4_ECOLI PF00163 ,PF01479
5 30S ribosomal protein S5 RS5_ECOLI PF00333 ,PF03719
6 30S ribosomal protein S6 RS6_ECOLI PF01250
7 30S ribosomal protein S7 RS7_ECOLI PF00177
8 30S ribosomal protein S8 RS8_ECOLI PF00410
9 30S ribosomal protein S9 RS9_ECOLI PF00380
10 30S ribosomal protein S10 RS10_ECOLI PF00338
11 30S ribosomal protein S11 RS11_ECOLI PF00411
12 30S ribosomal protein S12 RS12_ECOLI PF00164
13 30S ribosomal protein S13 RS13_ECOLI PF00416
14 30S ribosomal protein S14 RS14_ECOLI PF00253
15 30S ribosomal protein S15 RS15_ECOLI PF00312
16 30S ribosomal protein S16 RS16_ECOLI PF00886
27 30S ribosomal protein S17 RS17_ECOLI PF00366
28 30S ribosomal protein S18 RS18_ECOLI PF01084
29 30S ribosomal protein S19 RS19_ECOLI PF00203
20 30S ribosomal protein S20 RS20_ECOLI PF01649
21 30S ribosomal protein S21 RS21_ECOLI PF01165

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 50S large subunit components

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

Table of Human small Ribosomal subunits

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

See also

References

  1. ^ Rodnina MV, Wintermeyer W (2011). "The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation". Biochem Soc Trans. 39 (2): 658–62. doi:10.1042/BST0390658. PMID 21428957.
  2. ^ a b 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. PMID 24524803. Cite error: The named reference "pmid24524803" was defined multiple times with different content (see the help page).
  3. ^ Arnold RJ, Reilly JP (Apr 1999). "Observation of Escherichia coli ribosomal proteins and their posttranslational modifications by mass spectrometry". Analytical Biochemistry. 269 (1). doi:10.1006/abio.1998.3077. PMID 10094780.
  4. ^ Hamacher K, Trylska J, McCammon JA (Feb 2006). "Dependency map of proteins in the small ribosomal subunit". PLoS Computational Biology. 2 (2). doi:10.1371/journal.pcbi.0020010. PMID 16485038.{{cite journal}}: CS1 maint: unflagged free DOI (link)

Further reading

  • Korobeinikova AV, Garber MB, Gongadze GM (Jun 2012). "Ribosomal proteins: structure, function, and evolution". Biochemistry (Moscow). 77 (6): 562–74. doi:10.1134/S0006297912060028. PMID 22817455.
  • 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. PMID 24524803.

External links

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