This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3au7

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the ZRD-deleted mutant of TiaS in complex with agmatine

Structural highlights

3au7 is a 1 chain structure with sequence from Archaeoglobus fulgidus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TIAS_ARCFU ATP-dependent agmatine transferase that catalyzes the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2), converting the codon specificity from AUG to AUA.^[1]

Publication Abstract from PubMed

The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm(2)C is synthesized by tRNA(Ile)-agm(2)C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNA(Ile2) and tRNA(Met). In the TiaS-tRNA(Ile2)-ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP gamma-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm(2)C formation.

Structural basis of tRNA agmatinylation essential for AUA codon decoding.,Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T Nat Struct Mol Biol. 2011 Oct 16;18(11):1275-80. doi: 10.1038/nsmb.2144. PMID:22002223^[2]

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

References

↑ Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol. 2010 Apr;6(4):277-82. doi: 10.1038/nchembio.323. Epub 2010 Feb 7. PMID:20139989 doi:10.1038/nchembio.323
↑ Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T. Structural basis of tRNA agmatinylation essential for AUA codon decoding. Nat Struct Mol Biol. 2011 Oct 16;18(11):1275-80. doi: 10.1038/nsmb.2144. PMID:22002223 doi:10.1038/nsmb.2144

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3au7"

Categories: Archaeoglobus fulgidus | Large Structures | Numata T | Osawa T

@@ Line 1: / Line 1: @@
-[[Image:3au7.png|left|200px]]
-<!--
+==Crystal structure of the ZRD-deleted mutant of TiaS in complex with agmatine==
-The line below this paragraph, containing "STRUCTURE_3au7", creates the "Structure Box" on the page.
+<StructureSection load='3au7' size='340' side='right'caption='[[3au7]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3au7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AU7 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene></td></tr>
-{{STRUCTURE_3au7|  PDB=3au7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3au7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3au7 OCA], [https://pdbe.org/3au7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3au7 RCSB], [https://www.ebi.ac.uk/pdbsum/3au7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3au7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TIAS_ARCFU TIAS_ARCFU] ATP-dependent agmatine transferase that catalyzes the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2), converting the codon specificity from AUG to AUA.<ref>PMID:20139989</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm(2)C is synthesized by tRNA(Ile)-agm(2)C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNA(Ile2) and tRNA(Met). In the TiaS-tRNA(Ile2)-ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP gamma-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm(2)C formation.
-===Crystal structure of the ZRD-deleted mutant of TiaS in complex with agmatine===
+Structural basis of tRNA agmatinylation essential for AUA codon decoding.,Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T Nat Struct Mol Biol. 2011 Oct 16;18(11):1275-80. doi: 10.1038/nsmb.2144. PMID:22002223<ref>PMID:22002223</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[3au7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AU7 OCA].
+<div class="pdbe-citations 3au7" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Archaeoglobus fulgidus]]
-[[Category: Numata, T.]]
+[[Category: Large Structures]]
-[[Category: Osawa, T.]]
+[[Category: Numata T]]
-[[Category: Atp hydrolysis]]
+[[Category: Osawa T]]
-[[Category: Rna binding protein]]

3au7

From Proteopedia

Current revision

Crystal structure of the ZRD-deleted mutant of TiaS in complex with agmatine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox