Database accession: MF2120026
Name: Dihydrofolate reductase
PDB ID: 1cz3
Experimental method: X-ray (2.10 Å)
Assembly: Homodimer
Source organism: Thermotoga maritima
Primary 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
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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
dihydrofolate reductase activity dihydrofolate reductase activity
identical protein binding identical protein binding
NADP binding NADP binding
Biological process:
dihydrofolate metabolic process dihydrofolate metabolic process
folic acid metabolic process folic acid metabolic process
one-carbon metabolic process one-carbon metabolic process
tetrahydrofolate biosynthetic process tetrahydrofolate biosynthetic process
Cellular component:
cytosol cytosol
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Dihydrofolate reductase
Source organism: Thermotoga maritima
Length: 169 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVEKSHR
UniProtKB AC: Q60034 (positions: 2-165)
Coverage: 97%
Name: Dihydrofolate reductase
Source organism: Thermotoga maritima
Length: 169 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAKVIFVLAMDVSGKIASSVESWSSFEDRKNFRKITTEIGNVVMGRITFEEIGRPLPERLNVVLTRRPKTSNNPSLVFFNGSPADVVKFLEGKGYERVAVIGGKTVFTEFLREKLVDELFVTVEPYVFGKGIPFFDEFEGYFPLKLLEMRRLNERGTLFLKYSVEKSHR
UniProtKB AC: Q60034 (positions: 2-169)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
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).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
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). No related structure was found in the MFIB database.
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