1SOI

CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3

Summary for 1SOI

• Entry DOI: 10.2210/pdb1soi/pdb
• Descriptor: MutT/nudix family protein, SAMARIUM (III) ION (3 entities in total)
• Functional Keywords: nudix fold, alpha-beta-alpha sandwich, structural genomics, bsgc structure funded by nih, protein structure initiative, psi, berkeley structural genomics center, hydrolase
• Biological source: Deinococcus radiodurans
• Total number of polymer chains: 1
• Total formula weight: 18041.02

Authors

Ranatunga, W.,Hill, E.E.,Mooster, J.L.,Holbrook, E.L.,Schulze-Gahmen, U.,Xu, W.,Bessman, M.J.,Brenner, S.E.,Holbrook, S.R.,Berkeley Structural Genomics Center (BSGC) (deposition date: 2004-03-15, release date: 2004-05-11, Last modification date: 2024-02-14)

Primary citation

Ranatunga, W.,Hill, E.E.,Mooster, J.L.,Holbrook, E.L.,Schulze-Gahmen, U.,Xu, W.,Bessman, M.J.,Brenner, S.E.,Holbrook, S.R.
Structural Studies of the Nudix Hydrolase DR1025 From Deinococcus radiodurans and its Ligand Complexes.
J.Mol.Biol., 339:103-116, 2004

PubMed Abstract: We have determined the crystal structure, at 1.4A, of the Nudix hydrolase DR1025 from the extremely radiation resistant bacterium Deinococcus radiodurans. The protein forms an intertwined homodimer by exchanging N-terminal segments between chains. We have identified additional conserved elements of the Nudix fold, including the metal-binding motif, a kinked beta-strand characterized by a proline two positions upstream of the Nudix consensus sequence, and participation of the N-terminal extension in the formation of the substrate-binding pocket. Crystal structures were also solved of DR1025 crystallized in the presence of magnesium and either a GTP analog or Ap(4)A (both at 1.6A resolution). In the Ap(4)A co-crystal, the electron density indicated that the product of asymmetric hydrolysis, ATP, was bound to the enzyme. The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved.

PubMed: 15123424
DOI: 10.1016/j.jmb.2004.01.065

Experimental method

X-RAY DIFFRACTION (1.8 Å)