PDBsum entry: 2p4t

Oxidoreductase

PDB id: 2p4t

Contents

Protein chain

58 a.a.

Ligands

NAP

Waters ×78

PDB id:

2p4t

Name:

Oxidoreductase

Title:

Structure of the q67h mutant of r67 dihydrofolate reductase- NADP+ complex reveals a novel cofactor binding mode

Structure:

Dihydrofolate reductase type 2. Chain: a. Synonym: dihydrofolate reductase type ii. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: tmp-resistant, containing r67 dhfr overproducing plasmid plz1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.15Å R-factor: 0.193 R-free: 0.215

Authors:

N.Divya,E.Grifith,N.Narayana

Key ref:

N.Divya et al. (2007). Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode. Protein Sci, 16, 1063-1068. PubMed id: 17473013 DOI: 10.1110/ps.062740907

Date:

13-Mar-07 Release date: 05-Jun-07

Protein chain

P00383  (DYR21_ECOLX) -  Dihydrofolate reductase type 2

Seq: 78 a.a.

Struc: 58 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: 5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH

5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NAP) matches with 54.00% similarity) = 7,8-dihydrofolate + NADPH

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

 Gene Ontology (GO) functional annotation 

• Cellular component: plastid (1 term)
• Biological process: oxidation reduction (3 terms)
• Biochemical function: catalytic activity (2 terms)

reference

DOI no: 10.1110/ps.062740907

Protein Sci 16:1063-1068 (2007)

PubMed id: 17473013

Structure of the Q67H mutant of R67 dihydrofolate reductase-NADP+ complex reveals a novel cofactor binding mode.

N.Divya, E.Grifith, N.Narayana.

ABSTRACT

Plasmid-encoded bacterial R67 dihydrofolate reductase (DHFR) is a NADPH-dependent enzyme unrelated to chromosomal DHFR in amino acid sequence and structure. R67 DHFR is insensitive to the bacterial drug trimethoprim in contrast to chromosomal DHFR. The crystal structure of Q67H mutant of R67 DHFR bound to NADP(+) has been determined at 1.15 A resolution. The cofactor assumes an extended conformation with the nicotinamide ring bound near the center of the active site pore, the ribose and pyrophosphate group (PP(i)) extending toward the outer pore. The ribonicotinamide exhibits anti conformation as in chromosomal DHFR complexes. The relative orientation between the PP(i) and the nicotinamide ribose differs from that observed in chromosomal DHFR-NADP(+) complexes. The coenzyme displays symmetrical binding mode with several water-mediated hydrogen bonds with the protein besides ionic, stacking, and van der Waals interactions. The structure provides a molecular basis for the observed stoichiometry and cooperativity in ligand binding. The ternary model based on the present structure and the previous R67 DHFR-folate complex provides insight into the catalytic mechanism and indicates that the relative orientation of the reactants in plasmid DHFR is different from that seen in chromosomal DHFRs.

Selected figure(s)

Figure 2.
Figure 2. Omit difference Fourier map and environment of the bound cofactor. Fo # Fc omit map was computed using protein atoms

The above figure is reprinted by permission from the Protein Society: Protein Sci (2007, 16, 1063-1068) copyright 2007.

Figure was selected by an automated process.