PDBsum entry 1soi

Hydrolase

PDB id: 1soi

Contents

Protein chain

156 a.a. *

Metals

_SM ×3

Waters ×103

* Residue conservation analysis

PDB id:

1soi

Name:

Hydrolase

Title:

Crystal structure of nudix hydrolase dr1025 in complex with sm+3

Structure:

Mutt/nudix family protein. Chain: a. Engineered: yes

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Gene: dr1025. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å R-factor: 0.218 R-free: 0.251

Authors:

W.Ranatunga,E.E.Hill,J.L.Mooster,E.L.Holbrook,U.Schulze-Gahmen,W.Xu, M.J.Bessman,S.E.Brenner,S.R.Holbrook,Berkeley Structural Genomics Center (Bsgc)

Key ref:

W.Ranatunga et al. (2004). Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes. J Mol Biol, 339, 103-116. PubMed id: 15123424 DOI: 10.1016/j.jmb.2004.01.065

Date:

15-Mar-04 Release date: 11-May-04

Protein chain

Q9RVK2  (Q9RVK2_DEIRA) -  Nudix hydrolase DR_1025 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 159 a.a.

Struc: 156 a.a.

Enzyme reactions

• Enzyme class 2: E.C.3.6.1.61 - diadenosine hexaphosphate hydrolase (ATP-forming).
• Reaction:
  1. P₁,P₆-bis(5'-adenosyl) hexaphosphate + H2O = 2 ATP + 2 H⁺
  2. P₁,P₅-bis(5'-adenosyl) pentaphosphate + H2O = ADP + ATP + 2 H⁺
  3. P₁,P₄-bis(5'-adenosyl) tetraphosphate + H2O = AMP + ATP + 2 H⁺
• Cofactor: Divalent cation
• Enzyme class 3: E.C.3.6.1.69 - 8-oxo-(d)GTP phosphatase.
• Reaction:
  1. 8-oxo-GTP + H2O = 8-oxo-GDP + phosphate + H⁺
  2. 8-oxo-dGTP + H2O = 8-oxo-dGDP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2004.01.065

J Mol Biol 339:103-116 (2004)

PubMed id: 15123424

Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes.

W.Ranatunga, E.E.Hill, J.L.Mooster, E.L.Holbrook, U.Schulze-Gahmen, W.Xu, M.J.Bessman, S.E.Brenner, S.R.Holbrook.

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.

Selected figure(s)

Figure 1.
Figure 1. The structure of the DR1025 dimer as observed in the crystal. The Nudix box is colored in blue. Secondary structure elements are labeled. The b strands are colored yellow. The other a helices are in pink and the samarium bound to the Nudix helix (Sm1) is in orange. The intertwining N-terminal extension is in red. The proteins sit on a crystallographic 2-fold axis that relates the monomer to the dimer. Only one samarium of one monomer (Sm1) is shown.

Figure 3.
Figure 3. Electrostatic potential surface of the DR1025 dimer as calculated by the GRASP program.[32.] The areas of high negative charge are shaded red, while the positively charged regions are shaded blue.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 339, 103-116) copyright 2004.

Figures were selected by an automated process.