1DPZ

STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD711

Summary for 1DPZ

• Entry DOI: 10.2210/pdb1dpz/pdb
• Related: 1DR0 1DR8 1OSJ
• Descriptor: 3-ISOPROPYLMALATE DEHYDROGENASE (2 entities in total)
• Functional Keywords: dehydrogenase, minor groove, paperclip motion, oxidoreductase
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm: Q5SIY4
• Total number of polymer chains: 2
• Total formula weight: 74328.98

Authors

Nurachman, Z.,Akanuma, S.,Sato, T.,Oshima, T.,Tanaka, N. (deposition date: 1999-12-29, release date: 2000-01-12, Last modification date: 2023-08-09)

Primary citation

Nurachman, Z.,Akanuma, S.,Sato, T.,Oshima, T.,Tanaka, N.
Crystal structures of 3-isopropylmalate dehydrogenases with mutations at the C-terminus: crystallographic analyses of structure-stability relationships.
Protein Eng., 13:253-258, 2000

PubMed Abstract: Thermal stability of the Thermus thermophilus isopropylmalate dehydrogenase enzyme was substantially lost upon the deletion of three residues from the C-terminus. However, the stability was partly recovered by the addition of two, four and seven amino acid residues (called HD177, HD708 and HD711, respectively) to the C-terminal region of the truncated enzyme. Three structures of these mutant enzymes were determined by an X-ray diffraction method. All protein crystals belong to space group P2(1) and their structures were solved by a standard molecular replacement method where the original dimer structure of the A172L mutant was used as a search model. Thermal stability of these mutant enzymes is discussed based on the 3D structure with special attention to the width of the active-site groove and the minor groove, distortion of beta-sheet pillar structure and size of cavity in the domain-domain interface around the C-terminus. Our previous studies revealed that the thermal stability of isopropylmalate dehydrogenase increases when the active-site cleft is closed (the closed form). In the present study it is shown that the active-site cleft can be regulated by open-close movement of the minor groove located at the opposite side to the active-site groove on the same subunit, through a paperclip-like motion.

PubMed: 10810156
DOI: 10.1093/protein/13.4.253

Experimental method

X-RAY DIFFRACTION (2.8 Å)