3VVT

Crystal structure of reconstructed archaeal ancestral NDK, Arc1

Summary for 3VVT

• Entry DOI: 10.2210/pdb3vvt/pdb
• Related: 3VVU
• Descriptor: Nucleoside diphosphate kinase (2 entities in total)
• Functional Keywords: ndk, archaea, ancestor, transferase
• Total number of polymer chains: 2
• Total formula weight: 31298.34

Authors

Nemoto, N.,Miyazono, K.,Kimura, M.,Yokobori, S.,Akanuma, S.,Tanokura, M.,Yamagishi, A. (deposition date: 2012-07-27, release date: 2013-06-19, Last modification date: 2023-11-08)

Primary citation

Akanuma, S.,Nakajima, Y.,Yokobori, S.,Kimura, M.,Nemoto, N.,Mase, T.,Miyazono, K.,Tanokura, M.,Yamagishi, A.
Experimental evidence for the thermophilicity of ancestral life
Proc.Natl.Acad.Sci.USA, 110:11067-11072, 2013

PubMed Abstract: Theoretical studies have focused on the environmental temperature of the universal common ancestor of life with conflicting conclusions. Here we provide experimental support for the existence of a thermophilic universal common ancestor. We present the thermal stabilities and catalytic efficiencies of nucleoside diphosphate kinases (NDK), designed using the information contained in predictive phylogenetic trees, that seem to represent the last common ancestors of Archaea and of Bacteria. These enzymes display extreme thermal stabilities, suggesting thermophilic ancestries for Archaea and Bacteria. The results are robust to the uncertainties associated with the sequence predictions and to the tree topologies used to infer the ancestral sequences. Moreover, mutagenesis experiments suggest that the universal ancestor also possessed a very thermostable NDK. Because, as we show, the stability of an NDK is directly related to the environmental temperature of its host organism, our results indicate that the last common ancestor of extant life was a thermophile that flourished at a very high temperature.

PubMed: 23776221
DOI: 10.1073/pnas.1308215110

Experimental method

X-RAY DIFFRACTION (2.4 Å)