Crystal structure of 5′‐methylthioadenosine nucleosidase from <i>Arabidopsis thaliana</i> at 1.5‐Å resolution

Park, Eun Young; Oh, Seung Ick; Nam, Min Jung; Shin, Jeong Sheop; Kim, Kyung Nam; Song, Hyun Kyu

doi:10.1002/prot.21120

Cited by 11 publications

(10 citation statements)

References 18 publications

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“…We previously showed that AtMTAN1 forms a homodimer [37,51]. Like AtMTAN1, we recently found that AtMTAN2 is also able to form a homodimer (data not shown).…”

Section: Cbl3 Disrupts Homodimerization Of the Atmtan Proteinsmentioning

confidence: 88%

“…How can CBL3 decrease the AtMTAN enzyme activity? We believe that it has something to do with the fact that the AtMTAN proteins form homodimers, which appear to be important for the optimal enzyme activity [37,51]. Because the yeast three-hybrid assays revealed that AtMTANs fail to form homodimers in the presence of CBL3 (Fig.…”

Section: Cbl3 May Decrease the Enzyme Activity Of Atmtans By Hinderinmentioning

confidence: 95%

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Calcineurin B-like 3 calcium sensor associates with and inhibits 5′-methylthioadenosine nucleosidase 2 in Arabidopsis

Cho

et al. 2015

Plant Science

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“…We previously showed that AtMTAN1 forms a homodimer [37,51]. Like AtMTAN1, we recently found that AtMTAN2 is also able to form a homodimer (data not shown).…”

Section: Cbl3 Disrupts Homodimerization Of the Atmtan Proteinsmentioning

confidence: 88%

Section: Cbl3 May Decrease the Enzyme Activity Of Atmtans By Hinderinmentioning

confidence: 95%

Calcineurin B-like 3 calcium sensor associates with and inhibits 5′-methylthioadenosine nucleosidase 2 in Arabidopsis

Cho

et al. 2015

Plant Science

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“…The first structure of a representative plant MTAN from Arabidopsis thaliana (AtMTAN1) was determined recently in complex with the product, adenine (PDB code 2H8G). 24 To better understand the mechanisms of substrate-recognition and catalysis, we have examined the substrate specificities and activity of the two MTAN homologues present in A. thaliana, and have determined the structure of AtMTAN1 in its apo form, and in complex with the substrate-analogue, 5′-methylthiotubercidin (MTT), and the transition-state analogue, formycin A (FMA) (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

Molecular Determinants of Substrate Specificity in Plant 5′-Methylthioadenosine Nucleosidases

Siu¹,

Lee²,

Sufrin³

et al. 2008

Journal of Molecular Biology

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5'-Methylthioadenosine (MTA)/S-adenosylhomocysteine (SAH) nucleosidase (MTAN) is essential for cellular metabolism and development in many bacterial species. While the enzyme is found in plants, plant MTANs appear to select for MTA preferentially, with little or no affinity for SAH. To understand what determines substrate specificity in this enzyme, MTAN homologues from Arabidopsis thaliana (AtMTAN1 and AtMTAN2, which are referred to as AtMTN1 and AtMTN2 in the plant literature) have been characterized kinetically. While both homologues hydrolyze MTA with comparable kinetic parameters, only AtMTAN2 shows activity towards SAH. AtMTAN2 also has higher catalytic activity towards other substrate analogues with longer 5'-substituents. The structures of apo AtMTAN1 and its complexes with the substrate- and transition-state-analogues, 5'-methylthiotubercidin and formycin A, respectively, have been determined at 2.0-1.8 A resolution. A homology model of AtMTAN2 was generated using the AtMTAN1 structures. Comparison of the AtMTAN1 and AtMTAN2 structures reveals that only three residues in the active site differ between the two enzymes. Our analysis suggests that two of these residues, Leu181/Met168 and Phe148/Leu135 in AtMTAN1/AtMTAN2, likely account for the divergence in specificity of the enzymes. Comparison of the AtMTAN1 and available Escherichia coli MTAN (EcMTAN) structures suggests that a combination of differences in the 5'-alkylthio binding region and reduced conformational flexibility in the AtMTAN1 active site likely contribute to its reduced efficiency in binding substrate analogues with longer 5'-substituents. In addition, in contrast to EcMTAN, the active site of AtMTAN1 remains solvated in its ligand-bound forms. As the apparent pK(a) of an amino acid depends on its local environment, the putative catalytic acid Asp225 in AtMTAN1 may not be protonated at physiological pH and this suggests the transition state of AtMTAN1, like human MTA phosphorylase and Streptococcus pneumoniae MTAN, may be different from that found in EcMTAN.

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“…In monomers B and D, Glu202 assumes a single conformation not previously observed in any of the available MTAN structures (Singh et al, 2006; Siu et al, 2008a,b; Park et al, 2009, 2006; Lee et al, 2001, 2003, 2005). In monomers A and C, an additional conformation is observed at 40% occupancy (Fig.…”

Section: Resultsmentioning

confidence: 76%

“…This result was unexpected because when SAH was modeled into the crystal structures of At MTAN1, it appeared that residues in the 5′-alkylthio binding site would sterically clash with the homocysteinyl tail of SAH and no favourable electrostatic interactions could be established (Siu et al, 2008a; Park et al, 2006). To understand how SAH binds and why At MTAN1 cannot hydrolyze the substrate, the crystal structure of At MTAN1 in complex with SAH was determined.…”

Section: Discussionmentioning

confidence: 99%

Mechanism of substrate specificity in 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidases

Siu

Asmus

Zhang

et al. 2011

Journal of Structural Biology

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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 thaliana AtM-TAN1 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 2.2 Å 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.

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Crystal structure of 5′‐methylthioadenosine nucleosidase from Arabidopsis thaliana at 1.5‐Å resolution

Cited by 11 publications

References 18 publications

Calcineurin B-like 3 calcium sensor associates with and inhibits 5′-methylthioadenosine nucleosidase 2 in Arabidopsis

Calcineurin B-like 3 calcium sensor associates with and inhibits 5′-methylthioadenosine nucleosidase 2 in Arabidopsis

Molecular Determinants of Substrate Specificity in Plant 5′-Methylthioadenosine Nucleosidases

Mechanism of substrate specificity in 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidases

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