1q2s
From Proteopedia
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|PDB= 1q2s |SIZE=350|CAPTION= <scene name='initialview01'>1q2s</scene>, resolution 3.2Å | |PDB= 1q2s |SIZE=350|CAPTION= <scene name='initialview01'>1q2s</scene>, resolution 3.2Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=9DG:9-DEAZAGUANINE'>9DG</scene>, <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=PQ1:PHOSPHORIC+ACID+MONO-[5-(2-AMINO-5-AMINOMETHYL-4-OXO-3,5-DIHYDRO-4H-PYRIDO[2,3-D]PYRIMIDIN-8-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]+ESTER'>PQ1</scene>, <scene name='pdbligand=ROB:1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE'>ROB</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Queuine_tRNA-ribosyltransferase Queuine tRNA-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.29 2.4.2.29] </span> |
|GENE= TGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 Zymomonas mobilis]) | |GENE= TGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=542 Zymomonas mobilis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1q2r|1Q2R]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q2s OCA], [http://www.ebi.ac.uk/pdbsum/1q2s PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q2s RCSB]</span> | ||
}} | }} | ||
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[[Category: Liu, X.]] | [[Category: Liu, X.]] | ||
[[Category: Xie, W.]] | [[Category: Xie, W.]] | ||
| - | [[Category: 9DG]] | ||
| - | [[Category: ZN]] | ||
[[Category: covalent intermediat]] | [[Category: covalent intermediat]] | ||
[[Category: protein-rna complex]] | [[Category: protein-rna complex]] | ||
[[Category: tim barrel]] | [[Category: tim barrel]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:08:01 2008'' |
Revision as of 20:08, 30 March 2008
| |||||||
| , resolution 3.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , , | ||||||
| Gene: | TGT (Zymomonas mobilis) | ||||||
| Activity: | Queuine tRNA-ribosyltransferase, with EC number 2.4.2.29 | ||||||
| Related: | 1Q2R
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Overview
Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.
About this Structure
1Q2S is a Single protein structure of sequence from Zymomonas mobilis. Full crystallographic information is available from OCA.
Reference
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate., Xie W, Liu X, Huang RH, Nat Struct Biol. 2003 Oct;10(10):781-8. Epub 2003 Aug 31. PMID:12949492
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