3LGS

A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine

DOI: 10.2210/pdb3LGS/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-01-21 Released: 2010-06-30
Deposition Author(s): Siu, K.K.W., Howell, P.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.260
R-Value Work: 0.210
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Siu, K.K., Asmus, K., Zhang, A.N., Horvatin, C., Li, S., Liu, T., Moffatt, B., Woods, V.L., Howell, P.L.

(2011) J Struct Biol 173: 86-98

PubMed: 20554051 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.jsb.2010.06.006
Primary Citation of Related Structures:
3LGS

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.

Related Citations:

Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases.
Siu, K.K., Lee, J.E., Sufrin, J.R., Moffatt, B.A., McMillan, M., Cornell, K.A., Isom, C., Howell, P.L.
(2008) J Mol Biol 378: 112

Organizational Affiliation:

Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine nucleosidases	A, B, C, D	267	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At4g38800, atmtan1, MTN1, MTAN, MTAN1, T9A14.80 EC: 3.2.2.16
Find proteins for Q9T0I8 (Arabidopsis thaliana) Explore Q9T0I8 Go to UniProtKB: Q9T0I8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain I [B] SDF format, chain N [C] SDF format, chain Q [D] MOL2 format, chain E [A] MOL2 format, chain I [B] MOL2 format, chain N [C] MOL2 format, chain Q [D]	A, B, C, D	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Ligand Interaction
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain J [B] SDF format, chain O [C] SDF format, chain R [D] MOL2 format, chain F [A] MOL2 format, chain J [B] MOL2 format, chain O [C] MOL2 format, chain R [D]	A, B, C, D	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain H [A] SDF format, chain K [B] SDF format, chain L [B] SDF format, chain M [B] SDF format, chain P [C] SDF format, chain S [D] SDF format, chain T [D] SDF format, chain U [D] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain K [B] MOL2 format, chain L [B] MOL2 format, chain M [B] MOL2 format, chain P [C] MOL2 format, chain S [D] MOL2 format, chain T [D] MOL2 format, chain U [D]	A, B, C, D	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction