2c5s

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

Structural highlights

2c5s is a 1 chain structure with sequence from Bacillus anthracis str. Ames. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

THII_BACAN Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity).

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

ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This base acts as a sensitive trigger for the response mechanism to UV exposure, providing protection against its damaging effects. We present the crystal structure of Bacillus anthracis ThiI in complex with AMP, revealing an extended tripartite architecture in which an N-terminal ferredoxin-like domain (NFLD) connects the C-terminal catalytic PP-loop pyrophosphatase domain with a THUMP domain, an ancient predicted RNA-binding domain that is widespread in all kingdoms of life. We describe the structure of the THUMP domain, which appears to be unrelated to RNA-binding domains of known structure. Mapping the conserved residues of NFLD and the THUMP domain onto the ThiI structure suggests that these domains jointly form the tRNA-binding surface. The inaccessibility of U8 in the canonical L-shaped form of tRNA, and the existence of a glycine-rich linker joining the catalytic and RNA-binding moieties of ThiI suggest that structural changes may occur in both molecules upon binding.

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain.,Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA J Mol Biol. 2006 Feb 10;356(1):97-110. Epub 2005 Nov 22. PMID:16343540^[1]

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

References

↑ Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. J Mol Biol. 2006 Feb 10;356(1):97-110. Epub 2005 Nov 22. PMID:16343540 doi:http://dx.doi.org/10.1016/j.jmb.2005.11.013

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c5s"

@@ Line 3: / Line 3: @@
 <StructureSection load='2c5s' size='340' side='right'caption='[[2c5s]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c5s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_(strain_ames) Bacillus anthracis (strain ames)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C5S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c5s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_anthracis_str._Ames Bacillus anthracis str. Ames]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C5S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C5S FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=2c5s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c5s OCA], [https://pdbe.org/2c5s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c5s RCSB], [https://www.ebi.ac.uk/pdbsum/2c5s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c5s ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/THII_BACAN THII_BACAN] Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus anthracis str. Ames]]
 [[Category: Large Structures]]
-[[Category: Antson, A A]]
+[[Category: Antson AA]]
-[[Category: Fogg, M J]]
+[[Category: Fogg MJ]]
-[[Category: Koonin, E V]]
+[[Category: Koonin EV]]
-[[Category: Ortiz-Lombardia, M]]
+[[Category: Ortiz-Lombardia M]]
-[[Category: Waterman, D G]]
+[[Category: Waterman DG]]
-[[Category: 4-thiouridine synthase]]
-[[Category: Ferredoxin-like domain]]
-[[Category: Pp-loop pyrophosphatase domain]]
-[[Category: Rna binding protein]]
-[[Category: Rna-binding protein]]
-[[Category: Thiamine biosynthesis]]
-[[Category: Thump domain]]
-[[Category: Trna modification]]

2c5s

From Proteopedia

Current revision

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox