2uxb

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the context of the Thermus thermophilus 30S subunit.

Structural highlights

2uxb is a 10 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS7_THET8 One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B]

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

During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.

Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.,Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634^[1]

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

References

↑ Dunham CM, Selmer M, Phelps SS, Kelley AC, Suzuki T, Joseph S, Ramakrishnan V. Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. RNA. 2007 Jun;13(6):817-23. Epub 2007 Apr 6. PMID:17416634 doi:http://dx.doi.org/10.1261/rna.367307

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2uxb"

@@ Line 3: / Line 3: @@
 <StructureSection load='2uxb' size='340' side='right'caption='[[2uxb]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2uxb]] is a 23 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UXB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2uxb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UXB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fjg|1fjg]], [[1gix|1gix]], [[1i94|1i94]], [[1i95|1i95]], [[1i96|1i96]], [[1i97|1i97]], [[1ibk|1ibk]], [[1ibl|1ibl]], [[1ibm|1ibm]], [[1j5e|1j5e]], [[1jgo|1jgo]], [[1jgp|1jgp]], [[1jgq|1jgq]], [[1l1u|1l1u]], [[1n32|1n32]], [[1n33|1n33]], [[1n34|1n34]], [[1n36|1n36]], [[1pns|1pns]], [[1pnx|1pnx]], [[1xmo|1xmo]], [[1xmq|1xmq]], [[1xnq|1xnq]], [[1xnr|1xnr]], [[1yl4|1yl4]], [[2b64|2b64]], [[2b9m|2b9m]], [[2b9o|2b9o]], [[2f4v|2f4v]], [[2j00|2j00]], [[2j02|2j02]], [[2uu9|2uu9]], [[2uua|2uua]], [[2uub|2uub]], [[2uuc|2uuc]], [[2uxc|2uxc]], [[2uxd|2uxd]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2uxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uxb OCA], [https://pdbe.org/2uxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uxb RCSB], [https://www.ebi.ac.uk/pdbsum/2uxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uxb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[https://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[https://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[https://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B]
+[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 38: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thermus thermophilus]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Dunham, C M]]
+[[Category: Dunham CM]]
-[[Category: Joseph, S]]
+[[Category: Joseph S]]
-[[Category: Kelley, A C]]
+[[Category: Kelley AC]]
-[[Category: Phelps, S S]]
+[[Category: Phelps SS]]
-[[Category: Ramakrishnan, V]]
+[[Category: Ramakrishnan V]]
-[[Category: Selmer, M]]
+[[Category: Selmer M]]
-[[Category: Suzuki, T]]
+[[Category: Suzuki T]]
-[[Category: 30s ribosomal subunit]]
-[[Category: A site]]
-[[Category: Anticodon]]
-[[Category: Codon]]
-[[Category: Decoding]]
-[[Category: Frameshift]]
-[[Category: Frameshift suppressor trna]]
-[[Category: Messenger rna]]
-[[Category: Metal-binding]]
-[[Category: Mrna]]
-[[Category: Paromomycin]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Stem-loop]]
-[[Category: Transfer rna]]
-[[Category: Trna]]
-[[Category: Trna-binding]]
-[[Category: Zinc-finger]]

2uxb

From Proteopedia

Current revision

Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the context of the Thermus thermophilus 30S subunit.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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