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| | <StructureSection load='2zxi' size='340' side='right'caption='[[2zxi]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='2zxi' size='340' side='right'caption='[[2zxi]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zxi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zxi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZXI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zxh|2zxh]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aq_761 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=2zxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxi OCA], [https://pdbe.org/2zxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxi RCSB], [https://www.ebi.ac.uk/pdbsum/2zxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxi 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=2zxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zxi OCA], [https://pdbe.org/2zxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zxi RCSB], [https://www.ebi.ac.uk/pdbsum/2zxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zxi ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/MNMG_AQUAE MNMG_AQUAE]] NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34 (By similarity).[HAMAP-Rule:MF_00129]
| + | [https://www.uniprot.org/uniprot/MNMG_AQUAE MNMG_AQUAE] NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34 (By similarity).[HAMAP-Rule:MF_00129] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aquifex aeolicus huber and stetter 2001]] | + | [[Category: Aquifex aeolicus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Numata, T]] | + | [[Category: Numata T]] |
| - | [[Category: Osawa, T]] | + | [[Category: Osawa T]] |
| - | [[Category: 5-carboxymethylaminomethyl uridine]]
| + | |
| - | [[Category: Fad]]
| + | |
| - | [[Category: Fad-binding protein]]
| + | |
| - | [[Category: Modification]]
| + | |
| - | [[Category: Trna]]
| + | |
| - | [[Category: Trna modification enzyme]]
| + | |
| - | [[Category: Wobble uridine]]
| + | |
| Structural highlights
Function
MNMG_AQUAE NAD-binding protein involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm(5)s(2)U34 (By similarity).[HAMAP-Rule:MF_00129]
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 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at the anticodon first position occurs in tRNAs that read split codon boxes ending with purine. This modification is crucial for correct translation, by restricting codon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate in the cmnm(5)U modification process. Here we determined the crystal structure of Aquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tight interaction of GidA with FAD. Structure-based mutation analyses allowed us to identify two conserved Cys residues in the vicinity of the FAD-binding site that are essential for the cmnm(5)U modification in vivo. Together with mutational analysis of MnmE, we propose a mechanism for the cmnm(5)U modification process where GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism analogous to that of thymidylate synthase. We also present a tRNA-docking model that provides structural insights into the tRNA recognition mechanism for efficient modification.
Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon.,Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T Structure. 2009 May 13;17(5):713-24. PMID:19446527[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Osawa T, Ito K, Inanaga H, Nureki O, Tomita K, Numata T. Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure. 2009 May 13;17(5):713-24. PMID:19446527 doi:10.1016/j.str.2009.03.013
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