1K2E

crystal structure of a nudix protein from Pyrobaculum aerophilum

Summary for 1K2E

• Entry DOI: 10.2210/pdb1k2e/pdb
• Related: 1JRK 1K26
• Descriptor: NUDIX HOMOLOG, SULFATE ION, NICKEL (II) ION, ... (6 entities in total)
• Functional Keywords: nudix/mutt-like fold, mixed alpha/beta, dimer, putative nudix hydrolase, structural genomics, unknown function
• Biological source: Pyrobaculum aerophilum
• Total number of polymer chains: 2
• Total formula weight: 36609.32

Authors

Wang, S.,Mura, C.,Sawaya, M.R.,Cascio, D.,Eisenberg, D. (deposition date: 2001-09-26, release date: 2002-04-03, Last modification date: 2023-08-16)

Primary citation

Wang, S.,Mura, C.,Sawaya, M.R.,Cascio, D.,Eisenberg, D.
Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.
Acta Crystallogr.,Sect.D, 58:571-578, 2002

PubMed Abstract: Nudix proteins, formerly called MutT homolog proteins, are a large family of proteins that play an important role in reducing the accumulation of potentially toxic compounds inside the cell. They hydrolyze a wide variety of substrates that are mainly composed of a nucleoside diphosphate linked to some other moiety X and thus are called Nudix hydrolases. Here, the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum is reported. The structure was determined by the single-wavelength anomalous scattering method with data collected at the peak anomalous wavelength of an iridium-derivatized crystal. It reveals an extensive dimer interface, with each subunit contributing two strands to the beta-sheet of the other subunit. Individual subunits consist of a mixed highly twisted and curved beta-sheet of 11 beta-strands and two alpha-helices, forming an alpha-beta-alpha sandwich. The conserved Nudix box signature motif, which contains the essential catalytic residues, is located at the first alpha-helix and the beta-strand and loop preceding it. The unusually short connections between secondary-structural elements, together with the dimer form of the structure, are likely to contribute to the thermostability of the P. aerophilum Nudix protein.

PubMed: 11914479
DOI: 10.1107/S0907444902001191

Experimental method

X-RAY DIFFRACTION (1.8 Å)