Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
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.
Liao
Cheng-Jen
CJ
Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan, Republic of China.
Chin
Ko-Hsin
KH
Lin
Chao-Hsiung
CH
Tsai
Peter Shi-Fong
PS
Lyu
Ping-Chiang
PC
Young
Chiu-Chung
CC
Wang
Andrew H-J
AH
Chou
Shan-Ho
SH
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D003460:Crystallization; D018360:Crystallography, X-Ray; D034301:Deinococcus / Q000201:enzymology*; D007522:Isocitrate Lyase / Q000737:chemistry*; D007656:Ketoglutaric Acids / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017875:Phosphotransferases (Phosphomutases) / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment
D001426:Bacterial Proteins; D007656:Ketoglutaric Acids; D007522:Isocitrate Lyase; D017875:Phosphotransferases (Phosphomutases); C057167:phosphoenolpyruvate mutase