3LGS

A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine

Summary for 3LGS

• Entry DOI: 10.2210/pdb3lgs/pdb
• Related: 1JYS 1NC1 1NC3 2H8G 2QSU 2QTG 2QTT
• Descriptor: 5'-methylthioadenosine nucleosidases, S-ADENOSYL-L-HOMOCYSTEINE, ADENINE, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: Arabidopsis thaliana (mouse-ear cress,thale-cress)
• Total number of polymer chains: 4
• Total formula weight: 116539.54

Authors

Siu, K.K.W.,Howell, P.L. (deposition date: 2010-01-21, release date: 2010-06-30, Last modification date: 2024-02-21)

Primary citation

Siu, K.K.,Asmus, K.,Zhang, A.N.,Horvatin, C.,Li, S.,Liu, T.,Moffatt, B.,Woods, V.L.,Howell, P.L.
Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.
J.Struct.Biol., 173:86-98, 2011

PubMed Abstract: 5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2Å resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.

PubMed: 20554051
DOI: 10.1016/j.jsb.2010.06.006

Experimental method

X-RAY DIFFRACTION (2.2 Å)