PDBsum entry 5ccc

Oxidoreductase

PDB id: 5ccc

Contents

Protein chain

159 a.a.

Ligands

DDF

NAP

Waters ×134

PDB id:

5ccc

Name:

Oxidoreductase

Title:

Wild-type e.Coli dihydrofolate reductase complexed with 5,10- dideazatetrahydrofolate and oxidized nicotinamide adenine dinucleotide phosphate

Structure:

Dihydrofolate reductase. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: fola. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: dnay.

Resolution:

1.50Å R-factor: 0.175 R-free: 0.238

Authors:

D.Oyen,P.E.Wright

Key ref:

D.Oyen et al. (2015). Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway. J Am Chem Soc, 137, 9459-9468. PubMed id: 26147643 DOI: 10.1021/jacs.5b05707

Date:

01-Jul-15 Release date: 05-Aug-15

Protein chain

P0ABQ4  (DYR_ECOLI) -  Dihydrofolate reductase from Escherichia coli (strain K12)

Seq: 159 a.a.

Struc: 159 a.a.

Enzyme reactions

• Enzyme class: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = 7,8-dihydrofolate + NADPH + H(+)

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

reference

DOI no: 10.1021/jacs.5b05707

J Am Chem Soc 137:9459-9468 (2015)

PubMed id: 26147643

Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway.

D.Oyen, R.B.Fenwick, R.L.Stanfield, H.J.Dyson, P.E.Wright.

ABSTRACT

The enzyme dihydrofolate reductase (DHFR, E) from Escherichia coli is a paradigm for the role of protein dynamics in enzyme catalysis. Previous studies have shown that the enzyme progresses through the kinetic cycle by modulating the dynamic conformational landscape in the presence of substrate dihydrofolate (DHF), product tetrahydrofolate (THF), and cofactor (NADPH or NADP(+)). This study focuses on the quantitative description of the relationship between protein fluctuations and product release, the rate-limiting step of DHFR catalysis. NMR relaxation dispersion measurements of millisecond time scale motions for the E:THF:NADP(+) and E:THF:NADPH complexes of wild-type and the Leu28Phe (L28F) point mutant reveal conformational exchange between an occluded ground state and a low population of a closed state. The backbone structures of the occluded ground states of the wild-type and mutant proteins are very similar, but the rates of exchange with the closed excited states are very different. Integrated analysis of relaxation dispersion data and THF dissociation rates measured by stopped-flow spectroscopy shows that product release can occur by two pathways. The intrinsic pathway consists of spontaneous product dissociation and occurs for all THF-bound complexes of DHFR. The allosteric pathway features cofactor-assisted product release from the closed excited state and is utilized only in the E:THF:NADPH complexes. The L28F mutation alters the partitioning between the pathways and results in increased flux through the intrinsic pathway relative to the wild-type enzyme. This repartitioning could represent a general mechanism to explain changes in product release rates in other E. coli DHFR mutants.