3WKR image
Deposition Date 2013-10-30
Release Date 2014-07-16
Last Version Date 2022-08-24
Entry Detail
PDB ID:
3WKR
Keywords:
Title:
Crystal structure of the SepCysS-SepCysE complex from Methanocaldococcus jannaschii
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.24
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 65
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:O-phospho-L-seryl-tRNA:Cys-tRNA synthase
Gene (Uniprot):pscS
Chain IDs:A, B, E, F
Chain Length:416
Number of Molecules:4
Biological Source:Methanocaldococcus jannaschii
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein MJ1481
Gene (Uniprot):MJ1481
Chain IDs:C, D, G, H
Chain Length:216
Number of Molecules:4
Biological Source:Methanocaldococcus jannaschii
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
LLP A LYS ?
Primary Citation
Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea.
Proc.Natl.Acad.Sci.USA 111 10520 10525 (2014)
PMID: 25002468 DOI: 10.1073/pnas.1411267111

Abstact

Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)), which is converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). This represents the ancestral pathway of Cys biosynthesis and coding in archaea. Here we report a translation factor, SepCysE, essential for methanococcal Cys biosynthesis; its deletion in Methanococcus maripaludis causes Cys auxotrophy. SepCysE acts as a scaffold for SepRS and SepCysS to form a stable high-affinity complex for tRNA(Cys) causing a 14-fold increase in the initial rate of Cys-tRNA(Cys) formation. Based on our crystal structure (2.8-Å resolution) of a SepCysS⋅SepCysE complex, a SepRS⋅SepCysE⋅SepCysS structure model suggests that this ternary complex enables substrate channeling of Sep-tRNA(Cys). A phylogenetic analysis suggests coevolution of SepCysE with SepRS and SepCysS in the last universal common ancestral state. Our findings suggest that the tRNA-dependent Cys biosynthesis proceeds in a multienzyme complex without release of the intermediate and this mechanism may have facilitated the addition of Cys to the genetic code.

Legend

Protein

Chemical

Disease

Primary Citation of related structures