PDBsum entry 1f4l

Hydrolase

PDB id

1f4l

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Contents

			Protein chain

					545 a.a. *

			Ligands

					MET

			Metals

					_ZN

			Waters ×437

* Residue conservation analysis

PDB id:

1f4l

Links

Name:

Hydrolase

Title:

Crystal structure of the e.Coli methionyl-tRNA synthetase complexed with methionine

Structure:

Methionyl-tRNA synthetase. Chain: a. Fragment: residues 1-551. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: synthetic gene. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.85Å

R-factor:

0.182

R-free:

0.239

Authors:

L.Serre,G.Verdon,T.Chonowski,N.Hervouet,C.Zelwer

Key ref:

L.Serre et al. (2001). How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding. J Mol Biol, 306, 863-876. PubMed id: 11243794 DOI: 10.1006/jmbi.2001.4408

Date:

08-Jun-00

Release date:

21-Mar-01

PROCHECK

	Headers

	References

Protein chain

P00959 (SYM_ECOLI) - Methionine--tRNA ligase from Escherichia coli (strain K12)

Seq: Struc:

Seq: Struc:					677 a.a. 545 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.6.1.1.10 - methionine--tRNA ligase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

tRNA(Met) + L-methionine + ATP = L-methionyl-tRNA(Met) + AMP + diphosphate

tRNA(Met)

L-methionine
Bound ligand (Het Group name = MET)
corresponds exactly

ATP

L-methionyl-tRNA(Met)

AMP

diphosphate

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

reference

DOI no: 10.1006/jmbi.2001.4408	J Mol Biol 306:863-876 (2001)
PubMed id: 11243794

How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding.
L.Serre, G.Verdon, T.Choinowski, N.Hervouet, J.L.Risler, C.Zelwer.

ABSTRACT

Amino acid selection by aminoacyl-tRNA synthetases requires efficient mechanisms to avoid incorrect charging of the cognate tRNAs. A proofreading mechanism prevents Escherichia coli methionyl-tRNA synthetase (EcMet-RS) from activating in vivo L-homocysteine, a natural competitor of L-methionine recognised by the enzyme. The crystal structure of the complex between EcMet-RS and L-methionine solved at 1.8 A resolution exhibits some conspicuous differences with the recently published free enzyme structure. Thus, the methionine delta-sulphur atom replaces a water molecule H-bonded to Leu13N and Tyr260O(eta) in the free enzyme. Rearrangements of aromatic residues enable the protein to form a hydrophobic pocket around the ligand side-chain. The subsequent formation of an extended water molecule network contributes to relative displacements, up to 3 A, of several domains of the protein. The structure of this complex supports a plausible mechanism for the selection of L-methionine versus L-homocysteine and suggests the possibility of information transfer between the different functional domains of the enzyme.

Selected figure(s)



	Figure 6. Figure 6. Conformational changes in the area of helix aE and strand b5 with ball-and-stick representation for the complexed and free protein. The native protein is shown green and the complex is red.		Figure 8. Figure 8. Superimposition of the a-carbon backbones of the anticodon recognition domain for the free and the complexed Met-RS. The colour code is the same as that used in Figure 7.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20796028

H.Ingvarsson, and T.Unge (2010).
Flexibility and communication within the structure of the Mycobacterium smegmatis methionyl-tRNA synthetase.

FEBS J, 277, 3947-3962.

PDB codes:

2x1l 2x1m

19837083

E.Schmitt, I.C.Tanrikulu, T.H.Yoo, M.Panvert, D.A.Tirrell, and Y.Mechulam (2009).
Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity.

J Mol Biol, 394, 843-851.

PDB codes:

3h97 3h99 3h9b 3h9c

19706454

I.C.Tanrikulu, E.Schmitt, Y.Mechulam, W.A.Goddard, and D.A.Tirrell (2009).
Discovery of Escherichia coli methionyl-tRNA synthetase mutants for efficient labeling of proteins with azidonorleucine in vivo.

Proc Natl Acad Sci U S A, 106, 15285-15290.

18180246

N.Shen, M.Zhou, B.Yang, Y.Yu, X.Dong, and J.Ding (2008).
Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states.

Nucleic Acids Res, 36, 1288-1299.

PDB codes:

2quh 2qui 2quj 2quk

17510965

M.E.Budiman, M.H.Knaggs, J.S.Fetrow, and R.W.Alexander (2007).
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase.

Proteins, 68, 670-689.

17444518

R.Sathyapriya, and S.Vishveshwara (2007).
Structure networks of E. coli glutaminyl-tRNA synthetase: effects of ligand binding.

Proteins, 68, 541-550.

17378584

S.W.Lue, and S.O.Kelley (2007).
A single residue in leucyl-tRNA synthetase affecting amino acid specificity and tRNA aminoacylation.

Biochemistry, 46, 4466-4472.

16801548

A.J.Link, M.K.Vink, N.J.Agard, J.A.Prescher, C.R.Bertozzi, and D.A.Tirrell (2006).
Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids.

Proc Natl Acad Sci U S A, 103, 10180-10185.

15856481

J.Roach, S.Sharma, M.Kapustina, and C.W.Carter (2005).
Structure alignment via Delaunay tetrahedralization.

Proteins, 60, 66-81.

16189106

U.A.Ochsner, C.L.Young, K.C.Stone, F.B.Dean, N.Janjic, and I.A.Critchley (2005).
Mode of action and biochemical characterization of REP8839, a novel inhibitor of methionyl-tRNA synthetase.

Antimicrob Agents Chemother, 49, 4253-4262.

15388861

D.Datta, N.Vaidehi, D.Zhang, and W.A.Goddard (2004).
Selectivity and specificity of substrate binding in methionyl-tRNA synthetase.

Protein Sci, 13, 2693-2705.

12737824

L.D.Sherlin, and J.J.Perona (2003).
tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase.

Structure, 11, 591-603.

PDB code:

1nyl

12032090

K.J.Newberry, Y.M.Hou, and J.J.Perona (2002).
Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase.

EMBO J, 21, 2778-2787.

PDB codes:

1li5 1li7

11752401

K.L.Kiick, E.Saxon, D.A.Tirrell, and C.R.Bertozzi (2002).
Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation.

Proc Natl Acad Sci U S A, 99, 19-24.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.