2du7

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase

Structural highlights

2du7 is a 4 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SEPS_METJA Catalyzes the attachment of O-phosphoserine (Sep) to tRNA(Cys).^[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

Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.

Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.,Fukunaga R, Yokoyama S Nat Struct Mol Biol. 2007 Apr;14(4):272-9. Epub 2007 Mar 11. PMID:17351629^[2]

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

References

↑ Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR 3rd, Ibba M, Soll D. RNA-dependent cysteine biosynthesis in archaea. Science. 2005 Mar 25;307(5717):1969-72. PMID:15790858 doi:http://dx.doi.org/10.1126/science.1108329
↑ Fukunaga R, Yokoyama S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nat Struct Mol Biol. 2007 Apr;14(4):272-9. Epub 2007 Mar 11. PMID:17351629 doi:10.1038/nsmb1219

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2du7"

Categories: Large Structures | Methanocaldococcus jannaschii | Fukunaga R

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2du7.png|left|200px]]
-<!--
+==Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase==
-The line below this paragraph, containing "STRUCTURE_2du7", creates the "Structure Box" on the page.
+<StructureSection load='2du7' size='340' side='right'caption='[[2du7]], [[Resolution|resolution]] 3.60&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'>[[2du7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DU7 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]] 3.6&#8491;</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=2du7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2du7 OCA], [https://pdbe.org/2du7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2du7 RCSB], [https://www.ebi.ac.uk/pdbsum/2du7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2du7 ProSAT], [https://www.topsan.org/Proteins/RSGI/2du7 TOPSAN]</span></td></tr>
-{{STRUCTURE_2du7|  PDB=2du7  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SEPS_METJA SEPS_METJA] Catalyzes the attachment of O-phosphoserine (Sep) to tRNA(Cys).<ref>PMID:15790858</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/2du7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/main_output.php?pdb_ID=2du7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.
-===Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase===
+Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.,Fukunaga R, Yokoyama S Nat Struct Mol Biol. 2007 Apr;14(4):272-9. Epub 2007 Mar 11. PMID:17351629<ref>PMID:17351629</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2du7" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17351629}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17351629 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17351629}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DU7 is a [[Single protein]] structure of 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=2DU7 OCA].
-==Reference==
-Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea., Fukunaga R, Yokoyama S, Nat Struct Mol Biol. 2007 Apr;14(4):272-9. Epub 2007 Mar 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17351629 17351629]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Single protein]]
+[[Category: Fukunaga R]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-[[Category: Alpha4 tetramer]]
-[[Category: Ligase]]
-[[Category: National project on protein structural and functional analyse]]
-[[Category: Nppsfa]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan  7 20:07:31 2009''

2du7

From Proteopedia

Current revision

Crystal structure of Methanococcus jannacshii O-phosphoseryl-tRNA synthetase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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