PDBsum entry 1vbm

Ligase

PDB id: 1vbm

Contents

Protein chains

318 a.a. *

Ligands

SO4 ×4

YSA ×2

Waters ×88

* Residue conservation analysis

PDB id:

1vbm

Name:

Ligase

Title:

Crystal structure of the escherichia coli tyrosyl-tRNA synthetase complexed with tyr-ams

Structure:

Tyrosyl-tRNA synthetase. Chain: a, b. Fragment: residues 5-322. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.246 R-free: 0.284

Authors:

T.Kobayashi,K.Sakamoto,T.Takimura,K.Kamata,R.Sekine,S.Nishimura, S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

T.Kobayashi et al. (2005). Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. J Mol Biol, 346, 105-117. PubMed id: 15663931 DOI: 10.1016/j.jmb.2004.11.034

Date:

27-Feb-04 Release date: 25-Jan-05

Protein chains

P0AGJ9  (SYY_ECOLI) -  Tyrosine--tRNA ligase from Escherichia coli (strain K12)

Seq: 424 a.a.

Struc: 318 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.1 - tyrosine--tRNA ligase.
• Reaction: tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H⁺

tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) (Bound ligand (Het Group name = YSA) matches with 48.72% similarity) + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1016/j.jmb.2004.11.034

J Mol Biol 346:105-117 (2005)

PubMed id: 15663931

Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.

T.Kobayashi, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, K.Sakamoto, S.Nishimura, S.Yokoyama.

ABSTRACT

Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.

Selected figure(s)

Figure 6.
Figure 6. The Tyr-AMP binding sites of the TyrRSs. (a) The Tyr-AMP-binding site of the E. coli TyrRS·Tyr-AMS complex. (b) The corresponding view of the B. stearothermophilus TyrRS·Tyr-AMP complex5 (PDB ID: 3TS1). The carbon atoms of Tyr-AMS/Tyr-AMP are shown in light blue, and the hydrogen bonds are indicated by green broken lines. A phosphate atom is shown in green.

Figure 8.
Figure 8. Conformational changes of the KMSKS loop. (a) Open conformation of the KMSKS loop in the E. coli TyrRS·L-tyrosine structure. (b) Semi-open conformation of the KMSKS loop in the E. coil TyrRS·Tyr-AMS structure. The superposition of the open-form KMSKS loop is also shown by a pink translucent tube. (c) Closed conformation of the KMSKS loop in the T. thermophilus TyrRS·ATP·L-tyrosinol·tRNA^Tyr structure13 (PDB ID: 1H3E). The KMSKS loops are shown by orange tubes. The carbon atoms of L-tyrosine and L-tyrosinol are shown in pink, and those of Tyr-AMS are shown in light blue, respectively. (d) The bottleneck of the catalytic site in the T. thermophilus TyrRS closed form. The surface model of Tyr-AMP phosphate, which is a landmark of the aminoacyl transfer center, is shown by a stick model. (e) The 3'-adenosine of the tRNA cannot pass through the bottleneck of (d). The adenosine moiety is shown by a CPK model. (f) The exposed catalytic site in the E. coli TyrRS semi-open form. Tyr-AMS is shown by a stick model. The molecular surfaces were produced using the program MSMS (http://www.scripps.edu/mb/olson/people/sanner/html/msms_home.html).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 346, 105-117) copyright 2005.

Figures were selected by an automated process.