PDBsum entry 1zh6

Ligase

PDB id

1zh6

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Contents

			Protein chain

					307 a.a. *

			Ligands

					4AF


					BME ×2

			Waters ×80

* Residue conservation analysis

PDB id:

1zh6

Links

Name:

Ligase

Title:

Crystal structure of p-acetylphenylalanine-tRNA synthetase in complex with p-acetylphenylalanine

Structure:

Tyrosyl-tRNA synthetase. Chain: a. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes. Mutation: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: tyrs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.50Å

R-factor:

0.213

R-free:

0.278

Authors:

J.M.Turner,J.Graziano,G.Spraggon,P.G.Schultz

Key ref:

J.M.Turner et al. (2005). Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase. J Am Chem Soc, 127, 14976-14977. PubMed id: 16248607 DOI: 10.1021/ja0549042

Date:

22-Apr-05

Release date:

04-Apr-06

PROCHECK

	Headers

	References

Protein chain

Q57834 (SYY_METJA) - Tyrosine--tRNA ligase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: Struc:					306 a.a. 307 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.6.1.1.1 - tyrosine--tRNA ligase.

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

Reaction:

tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H⁺

tRNA(Tyr)

L-tyrosine
Bound ligand (Het Group name = 4AF)
matches with 75.00% similarity

ATP

L-tyrosyl-tRNA(Tyr)

AMP

diphosphate

H(+)

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

reference

DOI no: 10.1021/ja0549042	J Am Chem Soc 127:14976-14977 (2005)
PubMed id: 16248607

Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase.
J.M.Turner, J.Graziano, G.Spraggon, P.G.Schultz.

ABSTRACT

It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to allow genetic incorporation of unnatural amino acids into proteins in both prokaryotes and eukaryotes. Here we describe the crystal structure of an evolved aminoacyl-tRNA synthetase that charges the unnatural amino acid p-acetylphenylalanine. Molecular recognition is due to altered hydrogen bonding and packing interactions with bound substrate that result from changes in both side-chain and backbone conformation.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20307192

C.C.Liu, and P.G.Schultz (2010).
Adding new chemistries to the genetic code.

Annu Rev Biochem, 79, 413-444.

20217843

I.T.Yonemoto, and E.M.Tippmann (2010).
The juggernauts of biology.

Bioessays, 32, 314-321.

19666472

A.K.Antonczak, Z.Simova, and E.M.Tippmann (2009).
A critical examination of Escherichia coli esterase activity.

J Biol Chem, 284, 28795-28800.

19278648

K.Sakamoto, K.Murayama, K.Oki, F.Iraha, M.Kato-Murayama, M.Takahashi, K.Ohtake, T.Kobayashi, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2009).
Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography.

Structure, 17, 335-344.

PDB codes:

2z0z 2z10 2zxv

17878972

D.J.Maloney, N.Ghanem, J.Zhou, and S.M.Hecht (2007).
Positional assignment of differentially substituted bisaminoacylated pdCpAs.

Org Biomol Chem, 5, 3135-3138.

18000916

E.M.Tippmann, W.Liu, D.Summerer, A.V.Mack, and P.G.Schultz (2007).
A genetically encoded diazirine photocrosslinker in Escherichia coli.

Chembiochem, 8, 2210-2214.

PDB codes:

2q1g 2q1i 3d6u 3d6v

17322890

W.Liu, A.Brock, S.Chen, S.Chen, and P.G.Schultz (2007).
Genetic incorporation of unnatural amino acids into proteins in mammalian cells.

Nat Methods, 4, 239-244.

16618920

J.M.Turner, J.Graziano, G.Spraggon, and P.G.Schultz (2006).
Structural plasticity of an aminoacyl-tRNA synthetase active site.

Proc Natl Acad Sci U S A, 103, 6483-6488.

PDB codes:

1zh0 2ag6

16926858

J.Xie, and P.G.Schultz (2006).
A chemical toolkit for proteins--an expanded genetic code.

Nat Rev Mol Cell Biol, 7, 775-782.

16689635

L.Wang, J.Xie, and P.G.Schultz (2006).
Expanding the genetic code.

Annu Rev Biophys Biomol Struct, 35, 225-249.

16260173

J.Xie, and P.G.Schultz (2005).
Adding amino acids to the genetic repertoire.

Curr Opin Chem Biol, 9, 548-554.

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.