PDBsum entry 1rx8

Oxidoreductase

PDB id: 1rx8

Contents

Protein chain

159 a.a. *

Ligands

FOL

BME

NAP

Metals

_MN

Waters ×113

* Residue conservation analysis

PDB id:

1rx8

Name:

Oxidoreductase

Title:

Dihydrofolate reductase complexed with folate and 2'- monophosphoadenosine 5'-diphosphoribose

Structure:

Dihydrofolate reductase. Chain: a. Synonym: dhfr. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: rt500. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.144

Authors:

M.R.Sawaya

Key ref:

M.R.Sawaya and J.Kraut (1997). Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry, 36, 586-603. PubMed id: 9012674 DOI: 10.1021/bi962337c

Date:

25-Oct-96 Release date: 12-Mar-97

Protein chain

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

Seq: 159 a.a.

Struc: 159 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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) matches with 64.58% similarity) = 7,8-dihydrofolate (Bound ligand (Het Group name = FOL) corresponds exactly) + NADPH + H(+)

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

reference

DOI no: 10.1021/bi962337c

Biochemistry 36:586-603 (1997)

PubMed id: 9012674

Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence.

M.R.Sawaya, J.Kraut.

ABSTRACT

The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) cycles through five detectable kinetic intermediates: holoenzyme, Michaelis complex, ternary product complex, tetrahydrofolate (THF) binary complex, and THF.NADPH complex. Isomorphous crystal structures analogous to these five intermediates and to the transition state (as represented by the methotrexate-NADPH complex) have been used to assemble a 2.1 A resolution movie depicting loop and subdomain movements during the catalytic cycle (see Supporting Information). The structures suggest that the M20 loop is predominantly closed over the reactants in the holoenzyme, Michaelis, and transition state complexes. But, during the remainder of the cycle, when nicotinamide is not bound, the loop occludes (protrudes into) the nicotinamide-ribose binding pocket. Upon changing from the closed to the occluded conformation, the central portion of the loop rearranges from beta-sheet to 3(10) helix. The change may occur by way of an irregularly structured open loop conformation, which could transiently admit a water molecule into position to protonate N5 of dihydrofolate. From the Michaelis to the transition state analogue complex, rotation between two halves of ecDHFR, the adenosine binding subdomain and loop subdomain, closes the (p-aminobenzoyl)glutamate (pABG) binding crevice by approximately 0.5 A. Resulting enhancement of contacts with the pABG moiety may stabilize puckering at C6 of the pteridine ring in the transition state. The subdomain rotation is further adjusted by cofactor-induced movements (approximately 0.5 A) of helices B and C, producing a larger pABG cleft in the THF.NADPH analogue complex than in the THF analogue complex. Such movements may explain how THF release is assisted by NADPH binding. Subdomain rotation is not observed in vertebrate DHFR structures, but an analogous loop movement (residues 59-70) appears to similarly adjust the pABG cleft width, suggesting that these movements are important for catalysis. Loop movement, also unobserved in vertebrate DHFR structures, may preferentially weaken NADP+ vs NADPH binding in ecDHFR, an evolutionary adaptation to reduce product inhibition in the NADP+ rich environment of prokaryotes.