4H2U

Crystal structure of Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with cognate carrier protein and ATP

Summary for 4H2U

• Entry DOI: 10.2210/pdb4h2u/pdb
• Related: 3MF2 4H2S 4H2T 4H2V 4H2W 4H2X 4H2Y
• Descriptor: Amino acid--[acyl-carrier-protein] ligase 1, Aminoacyl carrier protein 1, ZINC ION, ... (9 entities in total)
• Functional Keywords: ligase, atp binding, glycine binding, carrier protein, aminoacyl-trna synthetase, seryl-trna synthetase.
• Biological source: Bradyrhizobium japonicum; More
• Total number of polymer chains: 4
• Total formula weight: 102617.56

Authors

Luic, M.,Weygand-Durasevic, I.,Ivic, N.,Mocibob, M. (deposition date: 2012-09-13, release date: 2013-03-06, Last modification date: 2013-05-29)

Primary citation

Mocibob, M.,Ivic, N.,Luic, M.,Weygand-Durasevic, I.
Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation.
Structure, 21:614-626, 2013

PubMed Abstract: Amino acid:[carrier protein] ligases (aa:CP ligases) are recently discovered enzymes that are highly similar to class II aminoacyl-tRNA synthetases (aaRSs). However, while aaRSs aminoacylate tRNA and supply building blocks for ribosomal translation, aa:CP ligases transfer activated amino acids to the phosphopantetheine group of small carrier proteins. We have solved the crystal structure of an aa:CP ligase complexed with the carrier protein (CP). The CP prosthetic group enters the active site from a different direction than tRNA in class II aaRS complexes through an idiosyncratic tunnel. CP binds to aa:CP ligase in a fundamentally different manner compared to tRNA binding by structurally closely related aaRSs. Based on crystallographic analysis, an enzyme of altered CP specificity was designed, and the mechanism of amino acid transfer to the prosthetic group was proposed. The presented study reveals how a conserved class II aaRS catalytic core can adapt to another function through minor structural alterations.

PubMed: 23541895
DOI: 10.1016/j.str.2013.02.017

Experimental method

X-RAY DIFFRACTION (2.1 Å)