5A60

Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two magnesium ions

Summary for 5A60

• Entry DOI: 10.2210/pdb5a60/pdb
• Related: 5A5Y 5A61 5A64 5A65 5A66 5A67 5A68
• Descriptor: INORGANIC TRIPHOSPHATASE, MAGNESIUM ION, TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: hydrolase, inorganic polyphosphate, tripolyphosphate, triphosphate tunnel metalloenzymes
• Biological source: ESCHERICHIA COLI K-12
• Total number of polymer chains: 1
• Total formula weight: 49068.71

Authors

Martinez, J.,Truffault, V.,Hothorn, M. (deposition date: 2015-06-23, release date: 2015-08-05, Last modification date: 2024-05-08)

Primary citation

Martinez, J.,Truffault, V.,Hothorn, M.
Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.
J.Biol.Chem., 290:23348-, 2015

PubMed Abstract: Triphosphate tunnel metalloenzymes (TTMs) are present in all kingdoms of life and catalyze diverse enzymatic reactions such as mRNA capping, the cyclization of adenosine triphosphate, the hydrolysis of thiamine triphosphate, and the synthesis and breakdown of inorganic polyphosphates. TTMs have an unusual tunnel domain fold that harbors substrate- and metal co-factor binding sites. It is presently poorly understood how TTMs specifically sense different triphosphate-containing substrates and how catalysis occurs in the tunnel center. Here we describe substrate-bound structures of inorganic polyphosphatases from Arabidopsis and Escherichia coli, which reveal an unorthodox yet conserved mode of triphosphate and metal co-factor binding. We identify two metal binding sites in these enzymes, with one co-factor involved in substrate coordination and the other in catalysis. Structural comparisons with a substrate- and product-bound mammalian thiamine triphosphatase and with previously reported structures of mRNA capping enzymes, adenylate cyclases, and polyphosphate polymerases suggest that directionality of substrate binding defines TTM catalytic activity. Our work provides insight into the evolution and functional diversification of an ancient enzyme family.

PubMed: 26221030
DOI: 10.1074/JBC.M115.674473

Experimental method

X-RAY DIFFRACTION (1.82 Å)