PDBsum entry 1dds

Oxidoreductase

PDB id: 1dds

Contents

Protein chains

159 a.a. *

Ligands

MTX ×2

Metals

_CL ×2

_CA

Waters ×121

* Residue conservation analysis

PDB id:

1dds

Name:

Oxidoreductase

Title:

Molecule: dihydrofolate reductase (E.C.1.5.1.3) complexed with methotrexate

Structure:

Dihydrofolate reductase. Chain: a, b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562.

Resolution:

2.20Å R-factor: 0.177 R-free: 0.200

Authors:

H.P.Yennawar,G.K.Farber

Key ref:

J.Dunbar et al. (1997). The effect of denaturants on protein structure. Protein Sci, 6, 1727-1733. PubMed id: 9260285 DOI: 10.1002/pro.5560060813

Date:

29-Jun-95 Release date: 15-Oct-95

Protein chains

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(+) = 7,8-dihydrofolate (Bound ligand (Het Group name = MTX) matches with 91.18% similarity) + NADPH + H(+)

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

reference

DOI no: 10.1002/pro.5560060813

Protein Sci 6:1727-1733 (1997)

PubMed id: 9260285

The effect of denaturants on protein structure.

J.Dunbar, H.P.Yennawar, S.Banerjee, J.Luo, G.K.Farber.

ABSTRACT

Virtually all studies of the protein-folding reaction add either heat, acid, or a chemical denaturant to an aqueous protein solution in order to perturb the protein structure. When chemical denaturants are used, very high concentrations are usually necessary to observe any change in protein structure. In a solution with such high denaturant concentrations, both the structure of the protein and the structure of the solvent around the protein can be altered. X-ray crystallography is the obvious experimental technique to probe both types of changes. In this paper, we report the crystal structures of dihydrofolate reductase with urea and of ribonuclease A with guanidinium chloride. These two classic denaturants have similar effects on the native structure of the protein. The most important change that occurs is a reduction in the overall thermal factor. These structures offer a molecular explanation for the reduction in mobility. Although the reduction is observed only with the native enzyme in the crystal, a similar decrease in mobility has also been observed in the unfolded state in solution (Makhatadze G, Privalov PL. 1992. Protein interactions with urea and guanidinium chloride: A calorimetric study.

Selected figure(s)

Figure 1.
Fig. 1. A: A artoon of the guanidinium 132- and 133-binding sites in ribonuclease. Gua forms a bond to Tyr 76, and Gua 132 forms a bond to Glu 9. In these cartoons, water molecules have been omitted for clarity. B: The urea 21 I-binding site in reductase. The A and designations refer to hetwo monomers in the asymmetric unit. As described n the text both urea and guanidinium form strong interactions which reduce the mobility of protein.

Figure 2.
Fig. 2. Electrondensityfor a guanidinium133intheribonucleasestruc- ture is shown.The 2F,, ~ F, mapwascontouredatthestandarddeviation ofthemap,andthemodel used togeneratethephasescontained no ua- nidinium. he distancebetweentheoxygenof Tyr 76andtheguanidinium nitrogen is only 2.5 A. Te distancebetweentheclosestnitrogensinGua 133 andGua132 s 3.3 A. The peptidebond of residue 62, whch is shown below Gua 133 inthisfigure, is further away. Thedistancesfor all ofthe proteininteractions with Gua 133areshon in Figure A.

The above figures are reprinted by permission from the Protein Society: Protein Sci (1997, 6, 1727-1733) copyright 1997.

Figures were selected by an automated process.