PDBsum entry 4rcv

Oxidoreductase

PDB id: 4rcv

Contents

Protein chains

370 a.a.

Ligands

NDP ×2

DE2

PO3 ×2

Metals

_MN ×2

Waters ×133

PDB id:

4rcv

Name:

Oxidoreductase

Title:

M. Tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase bound to 1-deoxy-l-erythrulose

Structure:

1-deoxy-d-xylulose 5-phosphate reductoisomerase. Chain: a, b. Fragment: unp residues 1-389. Synonym: dxp reductoisomerase, 1-deoxyxylulose-5-phosphate reductoisomerase, 2-c-methyl-d-erythritol 4-phosphate synthase. Engineered: yes

Source:

Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. Gene: dxr, p425_02990, rvbd_2870c. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.29Å R-factor: 0.176 R-free: 0.232

Authors:

A.M.Gulick,C.L.Allen,S.A.Kholodar,A.S.Murkin

Key ref:

S.A.Kholodar et al. (2015). The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces. J Am Chem Soc, 137, 2748-2756. PubMed id: 25642788 DOI: 10.1021/ja512911f

Date:

17-Sep-14 Release date: 18-Mar-15

Protein chains

P9WNS1  (DXR_MYCTU) -  1-deoxy-D-xylulose 5-phosphate reductoisomerase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 413 a.a.

Struc: 370 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.267 - 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
• Reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP⁺ = 1-deoxy-D-xylulose 5-phosphate + NADPH + H⁺

2-C-methyl-D-erythritol 4-phosphate (Bound ligand (Het Group name = DE2) matches with 53.85% similarity) + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 1-deoxy-D-xylulose 5-phosphate + NADPH + H(+)

• Cofactor: Mg(2+) or cobalt cation or Mn(2+)

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

reference

DOI no: 10.1021/ja512911f

J Am Chem Soc 137:2748-2756 (2015)

PubMed id: 25642788

The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces.

S.A.Kholodar, C.L.Allen, A.M.Gulick, A.S.Murkin.

ABSTRACT

Several mechanistically unrelated enzymes utilize the binding energy of their substrate's nonreacting phosphoryl group to accelerate catalysis. Evidence for the involvement of the phosphodianion in transition state formation has come from reactions of the substrate in pieces, in which reaction of a truncated substrate lacking its phosphorylmethyl group is activated by inorganic phosphite. What has remained unknown until now is how the phosphodianion group influences the reaction energetics at different points along the reaction coordinate. 1-Deoxy-d-xylulose-5-phosphate (DXP) reductoisomerase (DXR), which catalyzes the isomerization of DXP to 2-C-methyl-d-erythrose 4-phosphate (MEsP) and subsequent NADPH-dependent reduction, presents a unique opportunity to address this concern. Previously, we have reported the effect of covalently linked phosphate on the energetics of DXP turnover. Through the use of chemically synthesized MEsP and its phosphate-truncated analogue, 2-C-methyl-d-glyceraldehyde, the current study revealed a loss of 6.1 kcal/mol of kinetic barrier stabilization upon truncation, of which 4.4 kcal/mol was regained in the presence of phosphite dianion. The activating effect of phosphite was accompanied by apparent tightening of its interactions within the active site at the intermediate stage of the reaction, suggesting a role of the phosphodianion in disfavoring intermediate release and in modulation of the on-enzyme isomerization equilibrium. The results of kinetic isotope effect and structural studies indicate rate limitation by physical steps when the covalent linkage is severed. These striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme-phosphodianion interactions to the reaction coordinate.