PDBsum entry 2qtg

Hydrolase

PDB id: 2qtg

Contents

Protein chains

246 a.a. *

Ligands

MTH ×2

EDO ×2

Waters ×351

* Residue conservation analysis

PDB id:

2qtg

Name:

Hydrolase

Title:

Crystal structure of arabidopsis thaliana 5'-methylthioadenosine nucleosidase in complex with 5'-methylthiotubercidin

Structure:

5'-methylthioadenosine nucleosidase. Chain: a, b. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at4g38800. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.84Å R-factor: 0.185 R-free: 0.190

Authors:

K.K.W.Siu,P.L.Howell

Key ref:

K.K.Siu et al. (2008). Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases. J Mol Biol, 378, 112-128. PubMed id: 18342331 DOI: 10.1016/j.jmb.2008.01.088

Date:

02-Aug-07 Release date: 01-Apr-08

Protein chains

Q9T0I8  (MTN1_ARATH) -  5'-methylthioadenosine nucleosidase from Arabidopsis thaliana

Seq: 267 a.a.

Struc: 246 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.2.16 - methylthioadenosine nucleosidase.
• Reaction: S-methyl-5'-thioadenosine + H2O = 5-(methylsulfanyl)-D-ribose + adenine

S-methyl-5'-thioadenosine + H2O (Bound ligand (Het Group name = MTH) matches with 90.48% similarity) = 5-(methylsulfanyl)-D-ribose + adenine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2008.01.088

J Mol Biol 378:112-128 (2008)

PubMed id: 18342331

Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases.

K.K.Siu, J.E.Lee, J.R.Sufrin, B.A.Moffatt, M.McMillan, K.A.Cornell, C.Isom, P.L.Howell.

ABSTRACT

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.

Selected figure(s)

Figure 1.
Fig. 1. The structures of S-adenosylhomocysteine (SAH), 5′-methylthioadenosine (MTA), formycin A (FMA), 5′-methylthiotubercidin (MTT). For ease of comparison, the structures are numbered according to MTA rather than the IUPAC convention.

Figure 7.
Fig. 7. Conformational changes in the active sites of AtMTAN1 (a) and EcMTAN (b) upon binding of FMA or MTT. (c) Superimposition of EcMTAN-Ade and apo-AtMTAN1. Electron density is missing for the β10-α6 loop in EcMTAN because of disorder, so this region is not modeled in the structure and is represented here by a dotted line. (d) Superimposition of EcMTAN-MTT and AtMTAN1-MTT highlighting the positions of Phe148 in AtMTAN1 and Tyr107 in EcMTAN and their relative proximities to the 5′-alkylthio end of the ligand. In all panels, the apo- and MTT-bound structures of AtMTAN1 are shown in yellow and brown, respectively, while the ADE- and MTT-bound forms of EcMTAN are shown in gray and pink, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 378, 112-128) copyright 2008.

Figures were selected by an automated process.