2ZE3

Crystal Structure of DFA0005 Complexed with alpha-Ketoglutarate: A Novel Member of the ICL/PEPM Superfamily from Alkali-tolerant Deinococcus ficus

Summary for 2ZE3

• Entry DOI: 10.2210/pdb2ze3/pdb
• Descriptor: DFA0005, 2-OXOGLUTARIC ACID (3 entities in total)
• Functional Keywords: deinococcus ficus, organic waste left-over decomposition, alkaliphilic, icl/pepm superfamily, alpha-ketoglutarate ligand, isomerase
• Biological source: Deinococcus ficus
• Total number of polymer chains: 1
• Total formula weight: 29419.97

Authors

Liao, C.J.,Chin, K.H.,Chou, S.H. (deposition date: 2007-12-05, release date: 2008-08-12, Last modification date: 2024-03-13)

Primary citation

Liao, C.J.,Chin, K.H.,Lin, C.H.,Tsai, P.S.,Lyu, P.C.,Young, C.C.,Wang, A.H.,Chou, S.H.
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus
Proteins, 73:362-371, 2008

PubMed Abstract: The crystal structure of the DFA0005 protein complexed with alpha-ketoglutarate (AKG) from an alkali-tolerant bacterium Deinococcus ficus has been determined to a resolution of 1.62 A. The monomer forms an incomplete alpha7/beta8 barrel with a protruding alpha8 helix that interacts extensively with another subunit to form a stable dimer of two complete alpha8/beta8 barrels. The dimer is further stabilized by four glycerol molecules situated at the interface. One unique AKG ligand binding pocket per subunit is detected. Fold match using the DALI and SSE servers identifies DFA0005 as belonging to the isocitrate lyase/phosphoenolpyruvate mutase (ICL/PEPM) superfamily. However, further detailed structural and sequence comparison with other members in this superfamily and with other families containing AKG ligand indicate that DFA0005 protein exhibits considerable distinguishing features of its own and can be considered a novel member in this ICL/PEPM superfamily.

PubMed: 18433062
DOI: 10.1002/prot.22071

Experimental method

X-RAY DIFFRACTION (1.65 Å)