2HP3

Crystal structure of iminodisuccinate epimerase

Summary for 2HP3

• Entry DOI: 10.2210/pdb2hp3/pdb
• Related: 2HP0
• Descriptor: IDS-epimerase, 1,2-ETHANEDIOL, UNKNOWN ATOM OR ION, ... (5 entities in total)
• Functional Keywords: mmge/prpd fold, 6 helix bundle, chorismate mutase like, isomerase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 2
• Total formula weight: 97056.19

Authors

Lohkamp, B.,Bauerle, B.,Rieger, P.G.,Schneider, G. (deposition date: 2006-07-17, release date: 2006-09-12, Last modification date: 2023-08-30)

Primary citation

Lohkamp, B.,Bauerle, B.,Rieger, P.G.,Schneider, G.
Three-dimensional Structure of Iminodisuccinate Epimerase Defines the Fold of the MmgE/PrpD Protein Family.
J.Mol.Biol., 362:555-566, 2006

PubMed Abstract: Iminodisuccinate (IDS) epimerase catalyzes the epimerisation of R,R-, S,S- and R,S- iminodisuccinate, one step in the biodegradation of the chelating agent iminodisuccinate by Agrobacterium tumefaciens BY6. The enzyme is a member of the MmgE/PrpD protein family, a diverse and little characterized class of proteins of prokaryotic and eukaryotic origin. IDS epimerase does not show significant overall amino acid sequence similarity to any other protein of known three-dimensional structure. The crystal structure of this novel epimerase has been determined by multi-wavelength diffraction to 1.5 A resolution using selenomethionine-substituted enzyme. In the crystal, the enzyme forms a homo-dimer, and the subunit consists of two domains. The larger domain, not consecutive in sequence and comprising residues Met1-Lys266 and Leu400-Pro446, forms a novel all alpha-helical fold with a central six-helical bundle. The second, smaller domain folds into an alpha+beta domain, related in topology to chorismate mutase by a circular permutation. IDS epimerase is thus not related in three-dimensional structure to other known epimerases. The fold of the IDS epimerase is representative for the whole MmgE/PrpD family. The putative active site is located at the interface between the two domains of the subunit, and is characterized by a positively charged surface, consistent with the binding of a highly negatively charged substrate such as iminodisuccinate. Docking experiments suggest a two-base mechanism for the epimerisation reaction.

PubMed: 16934291
DOI: 10.1016/j.jmb.2006.07.051

Experimental method

X-RAY DIFFRACTION (1.71 Å)