PDBsum entry 2rh2

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Oxidoreductase PDB id
Protein chain
58 a.a.
MRD ×4
Waters ×133
PDB id:
Name: Oxidoreductase
Title: High resolution dhfr r-67
Structure: Dihydrofolate reductase type 2. Chain: a. Synonym: dihydrofolate reductase type ii. Engineered: yes
Source: Escherichia coli. Expressed in: escherichia coli. Other_details: tmp-resistant, containing r67 dhfr overproducing plasmid plz1
0.96Å     R-factor:   0.104     R-free:   0.117
Authors: J.M.Krahn,R.E.London
Key ref: J.M.Krahn et al. (2007). Crystal structure of a type II dihydrofolate reductase catalytic ternary complex. Biochemistry, 46, 14878-14888. PubMed id: 18052202 DOI: 10.1021/bi701532r
05-Oct-07     Release date:   03-Jun-08    
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Protein chain
Pfam   ArchSchema ?
P00383  (DYR21_ECOLX) -  Dihydrofolate reductase type 2
78 a.a.
58 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dihydrofolate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Folate Coenzymes
      Reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH
+ NADP(+)
= 7,8-dihydrofolate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     dihydrofolate reductase activity     1 term  


DOI no: 10.1021/bi701532r Biochemistry 46:14878-14888 (2007)
PubMed id: 18052202  
Crystal structure of a type II dihydrofolate reductase catalytic ternary complex.
J.M.Krahn, M.R.Jackson, E.F.DeRose, E.E.Howell, R.E.London.
Type II dihydrofolate reductase (DHFR) is a plasmid-encoded enzyme that confers resistance to bacterial DHFR-targeted antifolate drugs. It forms a symmetric homotetramer with a central pore which functions as the active site. Its unusual structure, which results in a promiscuous binding surface that accommodates either the dihydrofolate (DHF) substrate or the NADPH cofactor, has constituted a significant limitation to efforts to understand its substrate specificity and reaction mechanism. We describe here the first structure of a ternary R67 DHFR.DHF.NADP+ catalytic complex, resolved to 1.26 A. This structure provides the first clear picture of how this enzyme, which lacks the active site carboxyl residue that is ubiquitous in Type I DHFRs, is able to function. In the catalytic complex, the polar backbone atoms of two symmetry-related I68 residues provide recognition motifs that interact with the carboxamide on the nicotinamide ring, and the N3-O4 amide function on the pteridine ring. This set of interactions orients the aromatic rings of substrate and cofactor in a relative endo geometry in which the reactive centers are held in close proximity. Additionally, a central, hydrogen-bonded network consisting of two pairs of Y69-Q67-Q67'-Y69' residues provides an unusually tight interface, which appears to serve as a "molecular clamp" holding the substrates in place in an orientation conducive to hydride transfer. In addition to providing the first clear insight regarding how this extremely unusual enzyme is able to function, the structure of the ternary complex provides general insights into how a mutationally challenged enzyme, i.e., an enzyme whose evolution is restricted to four-residues-at-a-time active site mutations, overcomes this fundamental limitation.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19774544 A.Yahashiri, G.Nimrod, N.Ben-Tal, E.E.Howell, and A.Kohen (2009).
The effect of electrostatic shielding on H tunneling in R67 dihydrofolate reductase.
  Chembiochem, 10, 2620-2623.  
19549779 J.H.Davis, T.A.Baker, and R.T.Sauer (2009).
Engineering synthetic adaptors and substrates for controlled ClpXP degradation.
  J Biol Chem, 284, 21848-21855.  
18444258 A.Yahashiri, E.E.Howell, and A.Kohen (2008).
Tuning of the H-transfer coordinate in primitive versus well-evolved enzymes.
  Chemphyschem, 9, 980-982.  
18086667 S.Chopra, R.M.Dooling, C.G.Horner, and E.E.Howell (2008).
A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase.
  J Biol Chem, 283, 4690-4698.  
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