PDBsum entry 2odr

Ligase

PDB id: 2odr

Contents

Protein chains

491 a.a.

448 a.a. *

451 a.a. *

* Residue conservation analysis

PDB id:

2odr

Name:

Ligase

Title:

Methanococcus maripaludis phosphoseryl-tRNA synthetase

Structure:

Phosphoseryl-tRNA synthetase. Chain: a. Engineered: yes. Phosphoseryl-tRNA synthetase. Chain: b. Engineered: yes. Phosphoseryl-tRNA synthetase. Chain: c. Engineered: yes.

Source:

Methanococcus maripaludis. Organism_taxid: 267377. Strain: s2. Gene: mmp0688. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.23Å R-factor: 0.292 R-free: 0.306

Authors:

T.A.Steitz,S.Kamtekar

Key ref:

S.Kamtekar et al. (2007). Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase. Proc Natl Acad Sci U S A, 104, 2620-2625. PubMed id: 17301225 DOI: 10.1073/pnas.0611504104

Date:

26-Dec-06 Release date: 13-Feb-07

Protein chain

Q6LZE1  (SEPS_METMP) -  O-phosphoserine--tRNA(Cys) ligase from Methanococcus maripaludis (strain S2 / LL)

Seq: 537 a.a.

Struc: 491 a.a.*

Protein chains

Q6LZE1  (SEPS_METMP) -  O-phosphoserine--tRNA(Cys) ligase from Methanococcus maripaludis (strain S2 / LL)

Seq: 537 a.a.

Struc: 448 a.a.*

Protein chain

Q6LZE1  (SEPS_METMP) -  O-phosphoserine--tRNA(Cys) ligase from Methanococcus maripaludis (strain S2 / LL)

Seq: 537 a.a.

Struc: 451 a.a.*

* PDB and UniProt seqs differ at 187 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.6.1.1.27 - O-phosphoserine--tRNA ligase.
• Reaction: tRNA(Cys) + O-phospho-L-serine + ATP = O-phospho-L-seryl-tRNA(Cys) + AMP + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0611504104

Proc Natl Acad Sci U S A 104:2620-2625 (2007)

PubMed id: 17301225

Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase.

S.Kamtekar, M.J.Hohn, H.S.Park, M.Schnitzbauer, A.Sauerwald, D.Söll, T.A.Steitz.

ABSTRACT

A number of archaeal organisms generate Cys-tRNA(Cys) in a two-step pathway, first charging phosphoserine (Sep) onto tRNA(Cys) and subsequently converting it to Cys-tRNA(Cys). We have determined, at 3.2-A resolution, the structure of the Methanococcus maripaludis phosphoseryl-tRNA synthetase (SepRS), which catalyzes the first step of this pathway. The structure shows that SepRS is a class II, alpha(4) synthetase whose quaternary structure arrangement of subunits closely resembles that of the heterotetrameric (alphabeta)(2) phenylalanyl-tRNA synthetase (PheRS). Homology modeling of a tRNA complex indicates that, in contrast to PheRS, a single monomer in the SepRS tetramer may recognize both the acceptor terminus and anticodon of a tRNA substrate. Using a complex with tungstate as a marker for the position of the phosphate moiety of Sep, we suggest that SepRS and PheRS bind their respective amino acid substrates in dissimilar orientations by using different residues.

Selected figure(s)

Figure 2.
Fig. 2. The active site of M. maripaludis SepRS compared with that of T. thermophilus PheRS (PDB ID code 1JJC) (29). (A) The catalytic domain of one monomer of SepRS (cyan) is shown superposed on a catalytic domain of PheRS (gray). This superposition is used in all images. Residues mutated in SepRS are shown in stick representation. Residue labels in all images are colored to indicate the severity of the mutant phenotype, and corresponding residue numbers in PheRS are shown in brackets. (B) Three T. thermophilus PheRS residues that interact with the AMP moiety are shown in gray. The corresponding residues in M. maripaludis SepRS are conserved (green). (C) Four T. thermophilus PheRS residues that form a binding pocket for the phenylalanyl side chain are shown in gray. The corresponding residues in M. maripaludis SepRS (green) are incompatible with the binding of phenylalanine. (D) Residues in M. maripaludis SepRS that may interact with the phosphate moiety of phosphoserine. Difference electron density, caused by incubating a crystal with sodium tungstate and contoured at 6 , is shown as a mesh and superimposed on the structure both here and in F. (E and F) Side-by-side comparison of the interactions of T. thermophilus PheRS with phenylalanyl-adenylate and M. maripaludis SepRS with modeled phosphoseryl-adenylate. The side-chain conformations of M. maripaludis SepRS residues H186, T188, and R216 have been altered from the apo structure to accommodate the phosphoseryl moiety. The phosphoseryl phosphate group occupies a hydrophilic pocket, and its position overlaps the tungstate difference electron density.

Figure 3.
Fig. 3. tRNA^Phe homology modeled onto the structure of SepRS by using the superposition of the catalytic domains of M. maripaludis SepRS and T. thermophilus PheRS (19) illustrated in Fig. 1B. The tRNAs are shown as white/gray surfaces; each polypeptide chain of SepRS is colored differently, and interactions between SepRS and one of the tRNAs are labeled.

Figures were selected by an automated process.