3P8T: Crystal Structure Of The Archaeal Asparagine Synthetase A

Asparagine synthetase A (AsnA) catalyzes asparagine synthesis using aspartate, ATP, and ammonia as substrates. Asparagine is formed in two steps: the beta-carboxylate group of aspartate is first activated by ATP to form an aminoacyl-AMP before its amidation by a nucleophilic attack with an ammonium ion. Interestingly, this mechanism of amino acid activation resembles that used by aminoacyl-tRNA synthetases, which first activate the alpha-carboxylate group of the amino acid to form also an aminoacyl-AMP before they transfer the activated amino acid onto the cognate tRNA. In a previous investigation, we have shown that the open reading frame of Pyrococcus abyssi annotated as asparaginyl-tRNA synthetase (AsnRS) 2 is, in fact, an archaeal asparagine synthetase A (AS-AR) that evolved from an ancestral aspartyl-tRNA synthetase (AspRS). We present here the crystal structure of this AS-AR. The fold of this protein is similar to that of bacterial AsnA and resembles the catalytic cores of AspRS and AsnRS. The high-resolution structures of AS-AR associated with its substrates and end-products help to understand the reaction mechanism of asparagine formation and release. A comparison of the catalytic core of AS-AR with those of archaeal AspRS and AsnRS and with that of bacterial AsnA reveals a strong conservation. This study uncovers how the active site of the ancestral AspRS rearranged throughout evolution to transform an enzyme activating the alpha-carboxylate group into an enzyme that is able to activate the beta-carboxylate group of aspartate, which can react with ammonia instead of tRNA.
PDB ID: 3P8TDownload
MMDB ID: 92734
PDB Deposition Date: 2010/10/15
Updated in MMDB: 2011/09
Experimental Method:
x-ray diffraction
Resolution: 1.78  Å
Source Organism:
Similar Structures:
Biological Unit for 3P8T: dimeric; determined by author and by software (PISA)
Molecular Components in 3P8T
Label Count Molecule
Proteins (2 molecules)
Asns-like Asparaginyl-trna Synthetase Related Protein
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB