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.

2z2u

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 19:24, 9 February 2016

Crystal structure of archaeal TYW1

Structural highlights

2z2u is a 1 chain structure with sequence from Atcc 43067. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[TYW1_METJA] Component of the wyosine derivatives biosynthesis pathway that catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine (imG-14) on guanosine-37 of tRNA(Phe).[HAMAP-Rule:MF_01921]^[1]

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

Wyosine and its derivatives, such as wybutosine, found in eukaryotic and archaeal tRNAs, are tricyclic hypermodified nucleosides. In eukaryotes, wybutosine exists exclusively in position 37, 3'-adjacent to the anticodon, of tRNA(Phe), where it ensures correct translation by stabilizing the codon-anticodon base-pairing during the ribosomal decoding process. Recent studies revealed that the wyosine biosynthetic pathway consists of multistep enzymatic reactions starting from a guanosine residue. Among these steps, TYW1 catalyzes the second step to form the tricyclic ring structure, by cyclizing N(1)-methylguanosine. In this study, we solved the crystal structure of TYW1 from Methanocaldococcus jannaschii at 2.4 A resolution. TYW1 assumes an incomplete TIM barrel with (alpha/beta)(6) topology, which closely resembles the reported structures of radical SAM enzymes. Hence, TYW1 was considered to catalyze the cyclization reaction by utilizing the radical intermediate. Comparison with other radical SAM enzymes allowed us to build a model structure complexed with S-adenosylmethionine and two [4Fe-4S] clusters. Mutational analyses in yeast supported the validity of this complex model structure, which provides a structural insight into the radical reaction involving two [4Fe-4S] clusters to create a complex tricyclic base.

Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA.,Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R, Nureki O J Mol Biol. 2007 Oct 5;372(5):1204-14. Epub 2007 Jul 26. PMID:17727881^[2]

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

References

↑ Young AP, Bandarian V. Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine. Biochemistry. 2011 Dec 13;50(49):10573-5. doi: 10.1021/bi2015053. Epub 2011 Nov, 14. PMID:22026549 doi:http://dx.doi.org/10.1021/bi2015053
↑ Suzuki Y, Noma A, Suzuki T, Senda M, Senda T, Ishitani R, Nureki O. Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J Mol Biol. 2007 Oct 5;372(5):1204-14. Epub 2007 Jul 26. PMID:17727881 doi:10.1016/j.jmb.2007.07.024

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/2z2u"

Categories: Atcc 43067 | Ishitani, R | Nureki, O | Suzuki, Y | Metal binding protein

@@ Line 2: / Line 2: @@
 <StructureSection load='2z2u' size='340' side='right' caption='[[2z2u]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z2u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z2U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2z2u]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z2U FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z2u RCSB], [http://www.ebi.ac.uk/pdbsum/2z2u PDBsum]</span></td></tr>
+</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z2u OCA], [http://pdbe.org/2z2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z2u RCSB], [http://www.ebi.ac.uk/pdbsum/2z2u PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y257_METJA Y257_METJA]] Component of the wyosine derivatives biosynthesis pathway that catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine (imG-14) on guanosine-37 of tRNA(Phe).<ref>PMID:22026549</ref>
+[[http://www.uniprot.org/uniprot/TYW1_METJA TYW1_METJA]] Component of the wyosine derivatives biosynthesis pathway that catalyzes the condensation of N-methylguanine with 2 carbon atoms from pyruvate to form the tricyclic 4-demethylwyosine (imG-14) on guanosine-37 of tRNA(Phe).[HAMAP-Rule:MF_01921]<ref>PMID:22026549</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2z2u ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 25: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2z2u" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Methanocaldococcus jannaschii]]
+[[Category: Atcc 43067]]
 [[Category: Ishitani, R]]
 [[Category: Nureki, O]]
 [[Category: Suzuki, Y]]
 [[Category: Metal binding protein]]

2z2u

From Proteopedia

Revision as of 19:24, 9 February 2016

Crystal structure of archaeal TYW1

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