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5x6b

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Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus jannaschii

Structural highlights

5x6b is a 5 chain structure with sequence from Methanocaldococcus jannaschii DSM 2661. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.596Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPSS_METJA Converts O-phospho-L-seryl-tRNA(Cys) (Sep-tRNA(Cys)) to L-cysteinyl-tRNA(Cys) (Cys-tRNA(Cys)).^[1]

Publication Abstract from PubMed

Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA(Cys) followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA(Cys), respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNA(Cys) between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNA(Cys) synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code.

Structural basis for tRNA-dependent cysteine biosynthesis.,Chen M, Kato K, Kubo Y, Tanaka Y, Liu Y, Long F, Whitman WB, Lill P, Gatsogiannis C, Raunser S, Shimizu N, Shinoda A, Nakamura A, Tanaka I, Yao M Nat Commun. 2017 Nov 15;8(1):1521. doi: 10.1038/s41467-017-01543-y. PMID:29142195^[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
↑ Chen M, Kato K, Kubo Y, Tanaka Y, Liu Y, Long F, Whitman WB, Lill P, Gatsogiannis C, Raunser S, Shimizu N, Shinoda A, Nakamura A, Tanaka I, Yao M. Structural basis for tRNA-dependent cysteine biosynthesis. Nat Commun. 2017 Nov 15;8(1):1521. doi: 10.1038/s41467-017-01543-y. PMID:29142195 doi:http://dx.doi.org/10.1038/s41467-017-01543-y

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5x6b"

Categories: Large Structures | Methanocaldococcus jannaschii DSM 2661 | Chen M | Kato K | Yao M

@@ Line 3: / Line 3: @@
 <StructureSection load='5x6b' size='340' side='right'caption='[[5x6b]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5x6b]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X6B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5x6b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X6B FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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]] 2.596&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x6c|5x6c]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6b OCA], [http://pdbe.org/5x6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x6b RCSB], [http://www.ebi.ac.uk/pdbsum/5x6b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6b 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=5x6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6b OCA], [https://pdbe.org/5x6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x6b RCSB], [https://www.ebi.ac.uk/pdbsum/5x6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6b ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPSS_METJA SPSS_METJA] Converts O-phospho-L-seryl-tRNA(Cys) (Sep-tRNA(Cys)) to L-cysteinyl-tRNA(Cys) (Cys-tRNA(Cys)).<ref>PMID:15790858</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Chen, M]]
+[[Category: Methanocaldococcus jannaschii DSM 2661]]
-[[Category: Kato, K]]
+[[Category: Chen M]]
-[[Category: Yao, M]]
+[[Category: Kato K]]
-[[Category: Multidomain protein]]
+[[Category: Yao M]]
-[[Category: Rna binding protein-rna complex]]
-[[Category: Sepcyse]]

5x6b

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Current revision

Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus jannaschii

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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