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| - | {{STRUCTURE_4adv| PDB=4adv | SCENE= }} | |
| - | ===Structure of the E. coli methyltransferase KsgA bound to the E. coli 30S ribosomal subunit=== | |
| - | {{ABSTRACT_PUBMED_22308031}} | |
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| - | ==Function== | + | ==Structure of the E. coli methyltransferase KsgA bound to the E. coli 30S ribosomal subunit== |
| - | [[http://www.uniprot.org/uniprot/RS11_ECOLI RS11_ECOLI]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RS7_ECOLI RS7_ECOLI]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, where it has been shown to contact mRNA. Has been shown to contact tRNA in both the P and E sites; it probably blocks exit of the E site tRNA.<ref>PMID:2461734</ref> Protein S7 is also a translational repressor protein; it regulates the expression of the str operon members to different degrees by binding to its mRNA.<ref>PMID:2461734</ref> [[http://www.uniprot.org/uniprot/RS17_ECOLI RS17_ECOLI]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Also plays a role in translational accuracy; neamine-resistant ribosomes show reduced neamine-induced misreading in vitro.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/RSMA_ECOLI RSMA_ECOLI]] Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress.<ref>PMID:3905517</ref> <ref>PMID:19223326</ref> <ref>PMID:18990185</ref> [[http://www.uniprot.org/uniprot/RS18_ECOLI RS18_ECOLI]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/RS13_ECOLI RS13_ECOLI]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.<ref>PMID:15308780</ref> In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.<ref>PMID:15308780</ref> Contacts the tRNAs in the A and P sites.<ref>PMID:15308780</ref> The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs.<ref>PMID:15308780</ref> [[http://www.uniprot.org/uniprot/RS16_ECOLI RS16_ECOLI]] In addition to being a ribosomal protein, S16 also has a cation-dependent endonuclease activity.<ref>PMID:8730873</ref> In-frame fusions with the ribosome maturation factor rimM suppress mutations in the latter (probably due to increased rimM expression) and are found in translationally active 70S ribosomes.<ref>PMID:8730873</ref> [[http://www.uniprot.org/uniprot/RS6_ECOLI RS6_ECOLI]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_ECOLI RS3_ECOLI]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity).<ref>PMID:15652481</ref> Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref> [[http://www.uniprot.org/uniprot/RS9_ECOLI RS9_ECOLI]] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome.<ref>PMID:15308780</ref> [[http://www.uniprot.org/uniprot/RS12_ECOLI RS12_ECOLI]] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS14_ECOLI RS14_ECOLI]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site.[HAMAP-Rule:MF_00537] [[http://www.uniprot.org/uniprot/RS15_ECOLI RS15_ECOLI]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_01343] In the E.coli 70S ribosome it has been modeled (PubMed:12809609) to contact the 23S rRNA of the 50S subunit forming part of bridge B4. In the two 3.5 A resolved ribosome structures (PubMed:16272117) there are minor differences between side-chain conformations.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS20_ECOLI RS20_ECOLI]] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS8_ECOLI RS8_ECOLI]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_01302_B] Protein S8 is a translational repressor protein, it controls the translation of the spc operon by binding to its mRNA.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RS4_ECOLI RS4_ECOLI]] One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> Protein S4 is also a translational repressor protein, it controls the translation of the alpha-operon (which codes for S13, S11, S4, RNA polymerase alpha subunit, and L17) by binding to its mRNA.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> Also functions as a rho-dependent antiterminator of rRNA transcription, increasing the synthesis of rRNA under conditions of excess protein, allowing a more rapid return to homeostasis. Binds directly to RNA polymerase.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> [[http://www.uniprot.org/uniprot/RS10_ECOLI RS10_ECOLI]] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS19_ECOLI RS19_ECOLI]] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) it has been modeled to contact the 23S rRNA of the 50S subunit forming part of bridge B1a; this bridge is broken in the model with bound EF-G. The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:12859903), contacting alternately S13 or S19. In the 3.5 angstroms resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.[HAMAP-Rule:MF_00531] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. Contacts the A site tRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS5_ECOLI RS5_ECOLI]] With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).<ref>PMID:15652481</ref> Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.<ref>PMID:15652481</ref> The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref> | + | <SX load='4adv' size='340' side='right' viewer='molstar' caption='[[4adv]], [[Resolution|resolution]] 13.50Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[4adv]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ADV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ADV FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 13.5Å</td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4adv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4adv OCA], [https://pdbe.org/4adv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4adv RCSB], [https://www.ebi.ac.uk/pdbsum/4adv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4adv ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RS2_ECOLI RS2_ECOLI] |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation. |
| | | | |
| - | ==About this Structure==
| + | Structural Insights into Methyltransferase KsgA Function in 30S Ribosomal Subunit Biogenesis.,Boehringer D, O'Farrell HC, Rife JP, Ban N J Biol Chem. 2012 Mar 23;287(13):10453-9. Epub 2012 Feb 3. PMID:22308031<ref>PMID:22308031</ref> |
| - | [[4adv]] is a 22 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ADV OCA].
| + | |
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| - | ==See Also== | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | *[[Ribosomal protein S10|Ribosomal protein S10]]
| + | </div> |
| - | *[[Ribosomal protein S11|Ribosomal protein S11]]
| + | <div class="pdbe-citations 4adv" style="background-color:#fffaf0;"></div> |
| - | *[[Ribosomal protein S12|Ribosomal protein S12]]
| + | |
| - | *[[Ribosomal protein S14|Ribosomal protein S14]]
| + | |
| - | *[[Ribosomal protein S15|Ribosomal protein S15]]
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| - | *[[Ribosomal protein S16|Ribosomal protein S16]]
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| - | *[[Ribosomal protein S17|Ribosomal protein S17]]
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| - | *[[Ribosomal protein S19|Ribosomal protein S19]]
| + | |
| - | *[[Ribosomal protein S2|Ribosomal protein S2]]
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| - | *[[Ribosomal protein S20|Ribosomal protein S20]]
| + | |
| - | *[[Ribosomal protein S21|Ribosomal protein S21]]
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| - | *[[Ribosomal protein S3|Ribosomal protein S3]]
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| - | *[[Ribosomal protein S4|Ribosomal protein S4]]
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| - | *[[Ribosomal protein S5|Ribosomal protein S5]]
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| - | *[[Ribosomal protein S6|Ribosomal protein S6]]
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| - | *[[Ribosomal protein S7|Ribosomal protein S7]]
| + | |
| - | *[[Ribosomal protein S8|Ribosomal protein S8]]
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| - | *[[Ribosomal protein S9|Ribosomal protein S9]]
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| - | ==Reference== | + | ==See Also== |
| - | <ref group="xtra">PMID:022308031</ref><references group="xtra"/><references/>
| + | *[[Adenosine dimethyltransferase 3D structures|Adenosine dimethyltransferase 3D structures]] |
| | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </SX> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Ban, N.]] | + | [[Category: Large Structures]] |
| - | [[Category: Boehringer, D.]] | + | [[Category: Ban N]] |
| - | [[Category: Farrell, H C.O.]] | + | [[Category: Boehringer D]] |
| - | [[Category: Rife, J P.]] | + | [[Category: O'Farrell HC]] |
| - | [[Category: Ribosome biogenesis]] | + | [[Category: Rife JP]] |
| - | [[Category: Small ribosomal subunit]]
| + | |
| - | [[Category: Translation]]
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