PDBsum entry 2pyw

Transferase

PDB id: 2pyw

Contents

Protein chains

417 a.a. *

Ligands

SR1 ×2

ADP ×2

EDO ×5

Metals

_CL ×2

_MG ×5

Waters ×778

* Residue conservation analysis

PDB id:

2pyw

Name:

Transferase

Title:

Structure of a. Thaliana 5-methylthioribose kinase in complex with adp and mtr

Structure:

Uncharacterized protein. Chain: a, b. Synonym: at1g49820/f10f5_1. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: f10f5.1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.90Å R-factor: 0.165 R-free: 0.197

Authors:

S.Y.Ku

Key ref:

S.Y.Ku et al. (2007). Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog. Bmc Struct Biol, 7, 70-70. PubMed id: 17961230

Date:

16-May-07 Release date: 15-Jan-08

Protein chains

Q9C6D2  (MTK_ARATH) -  Methylthioribose kinase from Arabidopsis thaliana

Seq: 420 a.a.

Struc: 417 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.100 - S-methyl-5-thioribose kinase.
• Reaction: 5-(methylsulfanyl)-D-ribose + ATP = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate + ADP + H⁺

5-(methylsulfanyl)-D-ribose + ATP = 5-(methylsulfanyl)-alpha-D-ribose 1-phosphate (Bound ligand (Het Group name = ADP) corresponds exactly) + ADP + H(+)

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

Added reference

Bmc Struct Biol 7:70-70 (2007)

PubMed id: 17961230

Structure of Arabidopsis thaliana 5-methylthioribose kinase reveals a more occluded active site than its bacterial homolog.

S.Y.Ku, K.A.Cornell, P.L.Howell.

ABSTRACT

BACKGROUND: Metabolic variations exist between the methionine salvage pathway of humans and a number of plants and microbial pathogens. 5-Methylthioribose (MTR) kinase is a key enzyme required for methionine salvage in plants and many bacteria. The absence of a mammalian homolog suggests that MTR kinase is a good target for the design of specific herbicides or antibiotics. RESULTS: The structure of Arabidopsis thaliana MTR kinase co-crystallized with ATPgammaS and MTR has been determined at 1.9 A resolution. The structure is similar to B. subtilis MTR kinase and has the same protein kinase fold observed in other evolutionarily related protein kinase-like phosphotransferases. The active site is comparable between the two enzymes with the DXE-motif coordinating the nucleotide-Mg, the D238 of the HGD catalytic loop polarizing the MTR O1 oxygen, and the RR-motif interacting with the substrate MTR. Unlike its bacterial homolog, however, the Gly-rich loop (G-loop) of A. thaliana MTR kinase has an extended conformation, which shields most of the active site from solvent, a feature that resembles eukaryotic protein kinases more than the bacterial enzyme. The G- and W-loops of A. thaliana and B. subtilis MTR kinase adopt different conformations despite high sequence similarity. The ATPgammaS analog was hydrolyzed during the co-crystallization procedure, resulting in ADP in the active site. This suggests that the A. thaliana enzyme, like its bacterial homolog, may have significant ATPase activity in the absence of MTR. CONCLUSION: The structure of A. thaliana MTR kinase provides a template for structure-based design of agrochemicals, particularly herbicides whose effectiveness could be regulated by nutrient levels. Features of the MTR binding site offer an opportunity for a simple organic salt of an MTR analog to specifically inhibit MTR kinase.