General Information

Database accession: MF2120026

Name: Dihydrofolate reductase

PDB ID: 1cz3 PDB

Experimental method: X-ray (2.10 Å)

Assembly: homodimer

Source organism: Thermotoga maritima

Primer publication of the structure:

Dams T, Auerbach G, Bader G, Jacob U, Ploom T, Huber R, Jaenicke R
The crystal structure of dihydrofolate reductase from Thermotoga maritima: molecular features of thermostability.

(2000) J. Mol. Biol. 297: 659-72

PMID: 10731419 PubMed

Abstract:

Two high-resolution structures have been obtained for dihydrofolate reductase from the hyperthermophilic bacterium Thermotoga maritima in its unliganded state, and in its ternary complex with the cofactor NADPH and the inhibitor, methotrexate. While the overall fold of the hyperthermophilic enzyme is closely similar to monomeric mesophilic dihydrofolate reductase molecules, its quaternary structure is exceptional, in that T. maritima dihydrofolate reductase forms a highly stable homodimer. Here, the molecular reasons for the high intrinsic stability of the enzyme are elaborated and put in context with the available data on the physical parameters governing the folding reaction. The molecule is extremely rigid, even with respect to structural changes during substrate binding and turnover. Subunit cooperativity can be excluded from structural and biochemical data. Major contributions to the high intrinsic stability of the enzyme result from the formation of the dimer. Within the monomer, only subtle stabilizing interactions are detectable, without clear evidence for any of the typical increments of thermal stabilization commonly reported for hyperthermophilic proteins. The docking of the subunits is optimized with respect to high packing density in the dimer interface, additional salt-bridges and beta-sheets. The enzyme does not show significant structural changes upon binding its coenzyme, NADPH, and the inhibitor, methotrexate. The active-site loop, which is known to play an important role in catalysis in mesophilic dihydrofolate reductase molecules, is rearranged, participating in the association of the subunits; it no longer participates in catalysis.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

NADP binding Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. GeneOntology

dihydrofolate reductase activity Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+. GeneOntology

Biological process:

nucleotide biosynthetic process The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates). GeneOntology

oxidation-reduction process A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons. GeneOntology

glycine biosynthetic process The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid. GeneOntology

one-carbon metabolic process The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states. GeneOntology

tetrahydrofolate biosynthetic process The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group. GeneOntology

Cellular component: not assigned

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: A, B

Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.

Number of unique protein segments: 1


Chain A

Name: Dihydrofolate reductase

Source organism: Thermotoga maritima

Length: 164 residues

Sequence:Sequence according to PDB SEQRESAKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVE

UniProtKB AC: Q60034 (positions: 2-165) UniProt Coverage: 97%

UniRef90 AC: UniRef90_Q60034 (positions: 2-165) UniRef90

Chain B

Name: Dihydrofolate reductase

Source organism: Thermotoga maritima

Length: 164 residues

Sequence:Sequence according to PDB SEQRESAKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVE

UniProtKB AC: Q60034 (positions: 2-165) UniProt Coverage: 97%

UniRef90 AC: UniRef90_Q60034 (positions: 2-165) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Complex evidence:

The enzyme DHFR from the hyperthermophilic bacterium Thermotoga maritima represents an extremely stable dimer; no isolated structured monomers could be detected in equilibrium or during unfolding. The equilibrium unfolding strictly follows the two-state model for the dimer (PMID: 10413491).

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There is 1 related structure in the Protein Data Bank:





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