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- PDB-1wpl: Crystal structure of the inhibitory form of rat GTP cyclohydrolas... -

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Basic information

Entry
Database: PDB / ID: 1wpl
TitleCrystal structure of the inhibitory form of rat GTP cyclohydrolase I/GFRP complex
Components(GTP cyclohydrolase ...GTP cyclohydrolase I) x 2
KeywordsHYDROLASE/PROTEIN BINDING / ENZYME-REGULATORY PROTEIN COMPLEX / HYDROLASE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


dihydrobiopterin metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / GTP cyclohydrolase binding / pteridine-containing compound biosynthetic 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 ...dihydrobiopterin metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / GTP cyclohydrolase binding / pteridine-containing compound biosynthetic 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 / regulation of nitric oxide biosynthetic process / enzyme inhibitor activity / mitogen-activated protein kinase binding / dopamine biosynthetic process / negative regulation of cardiac muscle cell apoptotic process / amino acid binding / response to pain / positive regulation of heart rate / response to type II interferon / negative regulation of cellular senescence / response to tumor necrosis factor / tetrahydrofolate biosynthetic process / positive regulation of telomere maintenance via telomerase / negative regulation of blood pressure / regulation of blood pressure / vasodilation / positive regulation of neuron apoptotic process / melanosome / cytoplasmic vesicle / nuclear membrane / protein-containing complex assembly / response to lipopolysaccharide / GTPase activity / dendrite / calcium ion binding / protein-containing complex binding / GTP binding / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Gtp Cyclohydrolase I Feedback Regulatory Protein; Chain: K / GTP cyclohydrolase I feedback regulatory protein GFRP / GTP cyclohydrolase I, feedback regulatory protein / GFRP superfamily / GTP cyclohydrolase I feedback regulatory protein (GFRP) / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain ...Gtp Cyclohydrolase I Feedback Regulatory Protein; Chain: K / GTP cyclohydrolase I feedback regulatory protein GFRP / GTP cyclohydrolase I, feedback regulatory protein / GFRP superfamily / GTP cyclohydrolase I feedback regulatory protein (GFRP) / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP Cyclohydrolase I; Chain A, domain 1 / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIPHOSPHATE / 7,8-DIHYDROBIOPTERIN / GTP cyclohydrolase 1 / GTP cyclohydrolase 1 feedback regulatory protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMaita, N. / Hatakeyama, K. / Okada, K. / Hakoshima, T.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein
Authors: Maita, N. / Hatakeyama, K. / Okada, K. / Hakoshima, T.
History
DepositionSep 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP cyclohydrolase I
B: GTP cyclohydrolase I
C: GTP cyclohydrolase I
D: GTP cyclohydrolase I
E: GTP cyclohydrolase I
F: GTP cyclohydrolase I
G: GTP cyclohydrolase I
H: GTP cyclohydrolase I
I: GTP cyclohydrolase I
J: GTP cyclohydrolase I
K: GTP cyclohydrolase I feedback regulatory protein
L: GTP cyclohydrolase I feedback regulatory protein
M: GTP cyclohydrolase I feedback regulatory protein
N: GTP cyclohydrolase I feedback regulatory protein
O: GTP cyclohydrolase I feedback regulatory protein
P: GTP cyclohydrolase I feedback regulatory protein
Q: GTP cyclohydrolase I feedback regulatory protein
R: GTP cyclohydrolase I feedback regulatory protein
S: GTP cyclohydrolase I feedback regulatory protein
T: GTP cyclohydrolase I feedback regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,88560
Polymers355,02920
Non-polymers5,85640
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area91050 Å2
ΔGint-842 kcal/mol
Surface area86440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.720, 109.670, 130.270
Angle α, β, γ (deg.)90.00, 97.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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GTP cyclohydrolase ... , 2 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#1: Protein
GTP cyclohydrolase I / / GTP-CH-I


Mass: 25819.672 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P22288, GTP cyclohydrolase I
#2: Protein
GTP cyclohydrolase I feedback regulatory protein / P35


Mass: 9683.225 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P70552

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Non-polymers , 5 types, 270 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-HBI / 7,8-DIHYDROBIOPTERIN / Dihydrobiopterin


Mass: 239.231 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Chemical
ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H5O10P3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-propanol, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.282 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 83700 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 58.5 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.089 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.9 / Num. unique all: 12175 / Rsym value: 0.386 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IS7

1is7


Resolution: 2.8→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2328 4223 RANDOM
Rwork0.2069 --
all-83171 -
obs-78948 -
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22100 0 320 230 22650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.417
X-RAY DIFFRACTIONc_dihedral_angle_d23.81
X-RAY DIFFRACTIONc_improper_angle_d0.819
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3408 424 -
Rwork0.3123 --
obs-7868 100 %

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