3egv: Difference between revisions

Latest revision as of 13:03, 30 August 2023

Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11

Structural highlights

3egv is a 2 chain structure with sequence from Thermus thermophilus HB8. This structure supersedes the now removed PDB entry 3cju. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:	4MM, CL, GOL, IOD, SAH
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PRMA_THET8 Methylates ribosomal protein L11; this reaction probably occurs before the protein is assembled into the ribosome. This function is dispensable for growth and thermostability.

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

Ribosomal protein L11 is a universally conserved component of the large subunit, and plays a significant role during initiation, elongation, and termination of protein synthesis. In Escherichia coli, the lysine methyltransferase PrmA trimethylates the N-terminal alpha-amino group and the epsilon-amino groups of Lys3 and Lys39. Here, we report four PrmA-L11 complex structures in different orientations with respect to the PrmA active site. Two structures capture the L11 N-terminal alpha-amino group in the active site in a trimethylated post-catalytic state and in a dimethylated state with bound S-adenosyl-L-homocysteine. Two other structures show L11 in a catalytic orientation to modify Lys39 and in a noncatalytic orientation. The comparison of complex structures in different orientations with a minimal substrate recognition complex shows that the binding mode remains conserved in all L11 orientations, and that substrate orientation is brought about by the unusual interdomain flexibility of PrmA.

Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.,Demirci H, Gregory ST, Dahlberg AE, Jogl G Structure. 2008 Jul;16(7):1059-66. PMID:18611379^[1]

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

References

↑ Demirci H, Gregory ST, Dahlberg AE, Jogl G. Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure. 2008 Jul;16(7):1059-66. PMID:18611379 doi:10.1016/j.str.2008.03.016

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Demirci H, Gregory ST, Dahlberg AE, Jogl G. Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase. Structure. 2008 Jul;16(7):1059-66. PMID:18611379 doi:10.1016/j.str.2008.03.016

[1]

@@ Line 1: / Line 1: @@
 ==Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11==
-<StructureSection load='3egv' size='340' side='right' caption='[[3egv]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='3egv' size='340' side='right'caption='[[3egv]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3egv]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3cju 3cju]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EGV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EGV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3egv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3cju 3cju]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EGV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4MM:N,N,N-TRIMETHYLMETHIONINE'>4MM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 1.75&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2nxc|2nxc]], [[2nxe|2nxe]], [[2nxj|2nxj]], [[2nxn|2nxn]], [[3cju|3cju]], [[3cjs|3cjs]], [[3cjr|3cjr]], [[3cjq|3cjq]], [[3cjt|3cjt]], [[1ufk|1ufk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4MM:N,N,N-TRIMETHYLMETHIONINE'>4MM</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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=3egv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3egv OCA], [http://pdbe.org/3egv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3egv RCSB], [http://www.ebi.ac.uk/pdbsum/3egv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3egv ProSAT]</span></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=3egv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3egv OCA], [https://pdbe.org/3egv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3egv RCSB], [https://www.ebi.ac.uk/pdbsum/3egv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3egv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PRMA_THET8 PRMA_THET8]] Methylates ribosomal protein L11; this reaction probably occurs before the protein is assembled into the ribosome. This function is dispensable for growth and thermostability. [[http://www.uniprot.org/uniprot/RL11_THET8 RL11_THET8]] One of the L7 dimers in conjuction with L11 and its bound segment of 23S rRNA forms what is known as the L7/L12 stalk, which extends beyond the surface of the 70S ribosome. The stalk is preferentially stabilized in 70S versus 50S crystals.[HAMAP-Rule:MF_00736_B]  This protein binds directly to 23S ribosomal RNA.[HAMAP-Rule:MF_00736_B]  In the 70S ribosome is in a position where it could interact transiently with the A site tRNA during translation.[HAMAP-Rule:MF_00736_B]
+[https://www.uniprot.org/uniprot/PRMA_THET8 PRMA_THET8] Methylates ribosomal protein L11; this reaction probably occurs before the protein is assembled into the ribosome. This function is dispensable for growth and thermostability.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eg/3egv_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eg/3egv_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Ribosomal protein L11|Ribosomal protein L11]]
+*[[Ribosomal protein L11 3D structures|Ribosomal protein L11 3D structures]]
 *[[Ribosomal protein L11 methyltransferase|Ribosomal protein L11 methyltransferase]]
 == References ==
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Dahlberg, A E]]
+[[Category: Large Structures]]
-[[Category: Demirci, H]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Gregory, S T]]
+[[Category: Dahlberg AE]]
-[[Category: Jogl, G]]
+[[Category: Demirci H]]
-[[Category: Methylation]]
+[[Category: Gregory ST]]
-[[Category: Methyltransferase]]
+[[Category: Jogl G]]
-[[Category: Multiple methyltransferase]]
-[[Category: Post-translational modification]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Transferase]]
-[[Category: Transferase-ribosomal protein complex]]

3egv: Difference between revisions

Latest revision as of 13:03, 30 August 2023

Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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