PDBsum entry: 1zq1

Lyase

PDB id: 1zq1

Contents

Protein chains

437 a.a. *

508 a.a. *

Ligands

ASP ×2

Waters ×68

* Residue conservation analysis

PDB id:

1zq1

Name:

Lyase

Title:

Structure of gatde tRNA-dependent amidotransferase from pyrococcus abyssi

Structure:

Glutamyl-tRNA(gln) amidotransferase subunit d. Chain: a, b. Synonym: glu-adt subunit d. Engineered: yes. Glutamyl-tRNA(gln) amidotransferase subunit e. Chain: c, d. Synonym: glu-adt subunit e. Engineered: yes

Source:

Pyrococcus abyssi. Organism_taxid: 29292. Gene: gatd. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: gate.

Biol. unit:

Tetramer (from PQS)

Resolution:

3.00Å R-factor: 0.217 R-free: 0.256

Authors:

E.Schmitt,M.Panvert,S.Blanquet,Y.Mechulam

Key ref:

E.Schmitt et al. (2005). Structural basis for tRNA-dependent amidotransferase function. Structure, 13, 1421-1433. PubMed id: 16216574 DOI: 10.1016/j.str.2005.06.016

Date:

18-May-05 Release date: 18-Oct-05

Protein chains

Q9V0T9  (GATD_PYRAB) -  Glutamyl-tRNA(Gln) amidotransferase subunit D

Seq: 438 a.a.

Struc: 437 a.a.*

Protein chains

Q9V0U0  (GATE_PYRAB) -  Glutamyl-tRNA(Gln) amidotransferase subunit E

Seq: 633 a.a.

Struc: 508 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: cellular amino acid metabolic process (3 terms)
• Biochemical function: nucleotide binding (6 terms)

DOI no: 10.1016/j.str.2005.06.016

Structure 13:1421-1433 (2005)

PubMed id: 16216574

Structural basis for tRNA-dependent amidotransferase function.

E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam.

ABSTRACT

Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gln) is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNA(Gln) is then matured into Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase-that of GatDE from Pyrococcus abyssi. The 3.0 A resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE.

Selected figure(s)

Figure 1.
Figure 1. Tetrameric Organization of Proteins in the Asymmetric Unit
(A) Ribbon representation of the GatD dimer. Domains of the first subunit are drawn with dark colors, whereas domains of the second subunit are drawn with pale colors. N-terminal domains are in red or orange, and AnsA-like domains 1 are in yellow or pale yellow. AnsA-like domains 2 are in green or lime. These domains are labeled. In this figure and in the following ones, the asterisk indicates the NCS-related molecule. The two bound aspartate molecules are drawn with blue sticks.
(B) Ribbon representation of GatE molecules bound to the molecular surface of the GatD dimer. The orientation of this panel is rotated by 180° along a horizontal axis as compared to (A). GatD domains were colored as in (A). Domains of the first GatE subunit are drawn with dark colors, and domains of the second GatE* subunit are drawn with pale colors. The cradle domains are in dark blue or marine, the helical domains are in pink or white, and the AspRS-like domains are in cyan or pale blue.
(C) Molecular surface of the tetramer. The orientation was chosen to emphasize the docking of one molecule of GatE to a dimer of GatD. The cradle domain of GatE (dark blue) interacts with the N-terminal domain (red) and the AnsA-like domain 1 (yellow) of one subunit of the GatD dimer and with the AsnA-like domain2* (lime) of the second subunit. The color code is the same as in (A) and (B). Secondary structures were assigned with Procheck (Laskowski et al., 1993). Figure 1, Figure 2, Figure 3, Figure 4 and Figure 6 were drawn with Pymol (http://www.pymol.org).

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1421-1433) copyright 2005.

Figure was selected by the author.