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==The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui==
==The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui==
<StructureSection load='1vqn' size='340' side='right' caption='[[1vqn]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1vqn' size='340' side='right'caption='[[1vqn]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1vqn]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VQN FirstGlance]. <br>
<table><tr><td colspan='2'>[[1vqn]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VQN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=BTN:BIOTIN'>BTN</scene>, <scene name='pdbligand=HFA:ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC+ACID'>HFA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=BTN:BIOTIN'>BTN</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HFA:ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC+ACID'>HFA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PPU:PUROMYCIN-5-MONOPHOSPHATE'>PPU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1s72|1s72]], [[1jj2|1jj2]], [[1kqs|1kqs]], [[1m90|1m90]], [[1q7y|1q7y]], [[1q81|1q81]], [[1q82|1q82]], [[1q86|1q86]], [[1qvf|1qvf]], [[1qvg|1qvg]], [[1ffk|1ffk]], [[1ffz|1ffz]], [[1fgo|1fgo]], [[1vq4|1vq4]], [[1vq5|1vq5]], [[1vq6|1vq6]], [[1vq7|1vq7]], [[1vq8|1vq8]], [[1vq9|1vq9]], [[1vqk|1vqk]], [[1vql|1vql]], [[1vqm|1vqm]], [[1vqo|1vqo]], [[1vqp|1vqp]]</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=1vqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vqn OCA], [https://pdbe.org/1vqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vqn RCSB], [https://www.ebi.ac.uk/pdbsum/1vqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vqn ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vqn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vqn RCSB], [http://www.ebi.ac.uk/pdbsum/1vqn PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RL44_HALMA RL44_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331]  Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A]  Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A]  Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A]  Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL19_HALMA RL19_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]  
[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vq/1vqn_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vq/1vqn_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vqn ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 1vqn" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
Line 36: Line 37:
</StructureSection>
</StructureSection>
[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
[[Category: Schmeing, T M]]
[[Category: Large Structures]]
[[Category: Steitz, T A]]
[[Category: Schmeing TM]]
[[Category: Peptidyl transferase reaction]]
[[Category: Steitz TA]]
[[Category: Protein-protein complex]]
[[Category: Protein-rna complex]]
[[Category: Ribosome]]
[[Category: Ribosome 50]]
[[Category: Rna-rna complex]]

Latest revision as of 09:41, 23 August 2023

The structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortuiThe structure of CC-HPMN AND CCA-PHE-CAP-BIO bound to the large ribosomal subunit of haloarcula marismortui

Structural highlights

1vqn is a 10 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, , , , , , , , , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL2_HALMA One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The large ribosomal subunit catalyses the reaction between the alpha-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618-2620 (Escherichia coli numbering 2583-2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis.

An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.,Schmeing TM, Huang KS, Strobel SA, Steitz TA Nature. 2005 Nov 24;438(7067):520-4. PMID:16306996[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Schmeing TM, Huang KS, Strobel SA, Steitz TA. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature. 2005 Nov 24;438(7067):520-4. PMID:16306996 doi:10.1038/nature04152

1vqn, resolution 2.40Å

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