3t1h

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and Paromomycin

Structural highlights

3t1h is a 10 chain structure with sequence from Thermus thermophilus HB27 and 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 3.11Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS2_THET8 Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]

Publication Abstract from PubMed

Human tRNA(Lys3)(UUU) (htRNA(Lys3)(UUU)) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), 2-methylthio-N(6)-threonylcarbamoyladenosine (ms(2)t(6)A(37)), and pseudouridine (Psi(39)) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Psi(39)). Ribosome binding assays in vitro revealed that the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Psi(39) bound AAA and AAG codons, whereas binding of the unmodified ASL(Lys3)(UUU) was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Psi(39) enhanced the thermodynamic stability of the ASL through base stacking while ms(2)t(6)A(37) restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Psi(39) bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm(5)s(2)U(34) and ms(2)t(6)A(37) participate in the stability of the anticodon-codon interaction. Importantly, the mcm(5)s(2)U(34).G(3) wobble base pair is in the Watson-Crick geometry, requiring unusual hydrogen bonding to G in which mcm(5)s(2)U(34) must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.

Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism.,Vendeix FA, Murphy FV 4th, Cantara WA, Leszczynska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF J Mol Biol. 2011 Dec 29. PMID:22227389^[1]

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

References

↑ Vendeix FA, Murphy FV 4th, Cantara WA, Leszczynska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF. Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism. J Mol Biol. 2011 Dec 29. PMID:22227389 doi:10.1016/j.jmb.2011.12.048

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3t1h"

@@ Line 1: / Line 1: @@
-[[Image:3t1h.png|left|200px]]
-{{STRUCTURE_3t1h|  PDB=3t1h  |  SCENE=  }}
+==Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and Paromomycin==
+<StructureSection load='3t1h' size='340' side='right'caption='[[3t1h]], [[Resolution|resolution]] 3.11&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3t1h]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27] and [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=3T1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T1H FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.11&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=3t1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t1h OCA], [https://pdbe.org/3t1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t1h RCSB], [https://www.ebi.ac.uk/pdbsum/3t1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t1h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human tRNA(Lys3)(UUU) (htRNA(Lys3)(UUU)) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), 2-methylthio-N(6)-threonylcarbamoyladenosine (ms(2)t(6)A(37)), and pseudouridine (Psi(39)) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Psi(39)). Ribosome binding assays in vitro revealed that the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Psi(39) bound AAA and AAG codons, whereas binding of the unmodified ASL(Lys3)(UUU) was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Psi(39) enhanced the thermodynamic stability of the ASL through base stacking while ms(2)t(6)A(37) restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Psi(39) bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm(5)s(2)U(34) and ms(2)t(6)A(37) participate in the stability of the anticodon-codon interaction. Importantly, the mcm(5)s(2)U(34).G(3) wobble base pair is in the Watson-Crick geometry, requiring unusual hydrogen bonding to G in which mcm(5)s(2)U(34) must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.
-===Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and Paromomycin===
+Human tRNA(Lys3)(UUU) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism.,Vendeix FA, Murphy FV 4th, Cantara WA, Leszczynska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF J Mol Biol. 2011 Dec 29. PMID:22227389<ref>PMID:22227389</ref>
-{{ABSTRACT_PUBMED_22227389}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3t1h" style="background-color:#fffaf0;"></div>
-[[3t1h]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T1H OCA].
 ==See Also==
-*[[Ribosomal protein S10|Ribosomal protein S10]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-*[[Ribosomal protein S11|Ribosomal protein S11]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein S12|Ribosomal protein S12]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-*[[Ribosomal protein S13|Ribosomal protein S13]]
+== References ==
-*[[Ribosomal protein S14|Ribosomal protein S14]]
+<references/>
-*[[Ribosomal protein S15|Ribosomal protein S15]]
+__TOC__
-*[[Ribosomal protein S16|Ribosomal protein S16]]
+</StructureSection>
-*[[Ribosomal protein S17|Ribosomal protein S17]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S18|Ribosomal protein S18]]
+[[Category: Thermus thermophilus HB27]]
-*[[Ribosomal protein S19|Ribosomal protein S19]]
+[[Category: Thermus thermophilus HB8]]
-*[[Ribosomal protein S2|Ribosomal protein S2]]
+[[Category: Agris PF]]
-*[[Ribosomal protein S20|Ribosomal protein S20]]
+[[Category: Cantara W]]
-*[[Ribosomal protein S3|Ribosomal protein S3]]
+[[Category: Gustilo EM]]
-*[[Ribosomal protein S4|Ribosomal protein S4]]
+[[Category: Leszczynska G]]
-*[[Ribosomal protein S5|Ribosomal protein S5]]
+[[Category: Malkiewicz AAP]]
-*[[Ribosomal protein S6|Ribosomal protein S6]]
+[[Category: Murphy FV]]
-*[[Ribosomal protein S7|Ribosomal protein S7]]
+[[Category: Sproat B]]
-*[[Ribosomal protein S8|Ribosomal protein S8]]
+[[Category: Vendeix FAP]]
-*[[Ribosomal protein S9|Ribosomal protein S9]]
-*[[Ribosomal protein THX|Ribosomal protein THX]]
-==Reference==
-<ref group="xtra">PMID:022227389</ref><references group="xtra"/>
-[[Category: Thermus thermophilus]]
-[[Category: Agris, P F.]]
-[[Category: Cantara, W.]]
-[[Category: Gustilo, E M.]]
-[[Category: Leszczynska, G.]]
-[[Category: Malkiewicz, A A.P.]]
-[[Category: Murphy, F V.]]
-[[Category: Sproat, B.]]
-[[Category: Vendeix, F A.P.]]
-[[Category: Protein synthesis]]
-[[Category: Ribosome-antibiotic complex]]
-[[Category: Trna]]

3t1h

From Proteopedia

Current revision

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and Paromomycin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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