3REX

Crystal structure of the archaeal asparagine synthetase A complexed with Adenosine monophosphate

Summary for 3REX

• Entry DOI: 10.2210/pdb3rex/pdb
• Related: 1NNH 3P8T 3P8V 3P8Y 3REU
• Descriptor: AsnS-like asparaginyl-tRNA synthetase related protein, ADENOSINE MONOPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: asn synthetase, amp binding, anti parallel beat sheet, ligase
• Biological source: Pyrococcus abyssi
• Total number of polymer chains: 2
• Total formula weight: 68981.47

Authors

Blaise, M.,Frechin, M.,Charron, C.,Roy, H.,Sauter, C.,Lorber, B.,Olieric, V.,Kern, D. (deposition date: 2011-04-05, release date: 2011-08-17, Last modification date: 2023-09-13)

Primary citation

Blaise, M.,Frechin, M.,Olieric, V.,Charron, C.,Sauter, C.,Lorber, B.,Roy, H.,Kern, D.
Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.
J.Mol.Biol., 412:437-452, 2011

PubMed Abstract: Asparagine synthetase A (AsnA) catalyzes asparagine synthesis using aspartate, ATP, and ammonia as substrates. Asparagine is formed in two steps: the β-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 α-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 α-carboxylate group into an enzyme that is able to activate the β-carboxylate group of aspartate, which can react with ammonia instead of tRNA.

PubMed: 21820443
DOI: 10.1016/j.jmb.2011.07.050

Experimental method

X-RAY DIFFRACTION (1.8 Å)