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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11114 | |||||||||
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Title | inhibitory human GTP cyclohydrolase I - GFRP complex | |||||||||
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![]() | GTP cyclohydrolase GFTP / I / EC:3.5.4.16 / Tetrahydrobiopterin (BH4) synthesis / Cytosol / Zinc Ion Binding / Hydrolase Activity / Metal Ion Binding / Nucleotide Binding / allosteric inhibited / HYDROLASE | |||||||||
Function / homology | ![]() GTP cyclohydrolase binding / pteridine-containing compound biosynthetic process / dihydrobiopterin metabolic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / neuromuscular process controlling posture / negative regulation of biosynthetic process / GTP-dependent protein binding / regulation of removal of superoxide radicals ...GTP cyclohydrolase binding / pteridine-containing compound biosynthetic process / dihydrobiopterin metabolic process / regulation of lung blood pressure / GTP cyclohydrolase I / GTP cyclohydrolase I activity / neuromuscular process controlling posture / negative regulation of biosynthetic process / GTP-dependent protein binding / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / neuron projection terminus / regulation of nitric oxide biosynthetic process / mitogen-activated protein kinase binding / dopamine biosynthetic process / negative regulation of cardiac muscle cell apoptotic process / positive regulation of heart rate / response to pain / response to type II interferon / negative regulation of cellular senescence / response to tumor necrosis factor / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / positive regulation of telomere maintenance via telomerase / nitric oxide biosynthetic process / negative regulation of blood pressure / positive regulation of nitric-oxide synthase activity / regulation of blood pressure / vasodilation / positive regulation of neuron apoptotic process / melanosome / cytoplasmic vesicle / protein-containing complex assembly / nuclear membrane / response to lipopolysaccharide / GTPase activity / dendrite / calcium ion binding / protein-containing complex binding / GTP binding / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Ebenhoch R / Nar H | |||||||||
![]() | ![]() Title: A hybrid approach reveals the allosteric regulation of GTP cyclohydrolase I. Authors: Rebecca Ebenhoch / Simone Prinz / Susann Kaltwasser / Deryck J Mills / Robert Meinecke / Martin Rübbelke / Dirk Reinert / Margit Bauer / Lisa Weixler / Markus Zeeb / Janet Vonck / Herbert Nar / ![]() Abstract: Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). ...Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). Besides other roles, BH4 functions as cofactor in neurotransmitter biosynthesis. The BH4 biosynthetic pathway and GCH1 have been identified as promising targets to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). GFRP binds to GCH1 to form inhibited or activated complexes dependent on availability of cofactor ligands, BH4 and phenylalanine, respectively. We determined high-resolution structures of human GCH1-GFRP complexes by cryoelectron microscopy (cryo-EM). Cryo-EM revealed structural flexibility of specific and relevant surface lining loops, which previously was not detected by X-ray crystallography due to crystal packing effects. Further, we studied allosteric regulation of isolated GCH1 by X-ray crystallography. Using the combined structural information, we are able to obtain a comprehensive picture of the mechanism of allosteric regulation. Local rearrangements in the allosteric pocket upon BH4 binding result in drastic changes in the quaternary structure of the enzyme, leading to a more compact, tense form of the inhibited protein, and translocate to the active site, leading to an open, more flexible structure of its surroundings. Inhibition of the enzymatic activity is not a result of hindrance of substrate binding, but rather a consequence of accelerated substrate binding kinetics as shown by saturation transfer difference NMR (STD-NMR) and site-directed mutagenesis. We propose a dissociation rate controlled mechanism of allosteric, noncompetitive inhibition. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
Images | ![]() | 132.4 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z85MC ![]() 6z80C ![]() 6z86C ![]() 6z87C ![]() 6z88C ![]() 6z89C ![]() 7accC ![]() 7al9C ![]() 7alaC ![]() 7albC ![]() 7alcC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : inhibitory GCH1-GFRP complex (BH4 bound)
Entire | Name: inhibitory GCH1-GFRP complex (BH4 bound) |
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Components |
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-Supramolecule #1: inhibitory GCH1-GFRP complex (BH4 bound)
Supramolecule | Name: inhibitory GCH1-GFRP complex (BH4 bound) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 353 KDa |
-Macromolecule #1: GTP cyclohydrolase 1
Macromolecule | Name: GTP cyclohydrolase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: GTP cyclohydrolase I |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.32492 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHGSD DDDKRPEAKS AQPADGWKGE RPRSEEDNEL NLPNLAAAYS SILSSLGENP QRQGLLKTPW RAASAMQFFT KGYQETISD VLNDAIFDED HDEMVIVKDI DMFSMCEHHL VPFVGKVHIG YLPNKQVLGL SKLARIVEIY SRRLQVQERL T KQIAVAIT ...String: MHHHHHHGSD DDDKRPEAKS AQPADGWKGE RPRSEEDNEL NLPNLAAAYS SILSSLGENP QRQGLLKTPW RAASAMQFFT KGYQETISD VLNDAIFDED HDEMVIVKDI DMFSMCEHHL VPFVGKVHIG YLPNKQVLGL SKLARIVEIY SRRLQVQERL T KQIAVAIT EALRPAGVGV VVEATHMCMV MRGVQKMNSK TVTSTMLGVF REDPKTREEF LTLIRS UniProtKB: GTP cyclohydrolase 1 |
-Macromolecule #2: GTP cyclohydrolase 1 feedback regulatory protein
Macromolecule | Name: GTP cyclohydrolase 1 feedback regulatory protein / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 9.992483 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMPYLLIS TQIRMEVGPT MVGDEQSDPE LMQHLGASKR RALGNNFYEY YVDDPPRIVL DKLERRGFRV LSMTGVGQTL VWCLHKE UniProtKB: GTP cyclohydrolase 1 feedback regulatory protein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: 7,8-DIHYDROBIOPTERIN
Macromolecule | Name: 7,8-DIHYDROBIOPTERIN / type: ligand / ID: 4 / Number of copies: 10 / Formula: HBI |
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Molecular weight | Theoretical: 239.231 Da |
Chemical component information | ![]() ChemComp-HBI: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.25 mg/mL | |||||||||
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Buffer | pH: 5.75 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2688 / Average exposure time: 8.0 sec. / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |