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- PDB-1a8r: GTP CYCLOHYDROLASE I (H112S MUTANT) IN COMPLEX WITH GTP -

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Basic information

Entry
Database: PDB / ID: 1a8r
TitleGTP CYCLOHYDROLASE I (H112S MUTANT) IN COMPLEX WITH GTP
ComponentsGTP CYCLOHYDROLASE I
KeywordsHYDROLASE / GTP / PURINE HYDROLYSIS / PTERINE SYNTHESIS
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tRNA queuosine(34) biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / protein-containing complex / zinc ion binding / identical protein binding ...GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tRNA queuosine(34) biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / GTP binding / protein-containing complex / zinc ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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, 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
GUANOSINE-5'-TRIPHOSPHATE / GTP cyclohydrolase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsAuerbach, G. / Nar, H. / Bracher, A. / Bacher, A. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Biosynthesis of pteridines. Reaction mechanism of GTP cyclohydrolase I.
Authors: Rebelo, J. / Auerbach, G. / Bader, G. / Bracher, A. / Nar, H. / Hosl, C. / Schramek, N. / Kaiser, J. / Bacher, A. / Huber, R. / Fischer, M.
#1: Journal: Biol.Chem. / Year: 1997
Title: The Pathway from GTP to Tetrahydrobiopterin: Three-Dimensional Structures of GTP Cyclohydrolase I and 6-Pyruvoyl Tetrahydropterin Synthase
Authors: Auerbach, G. / Nar, H.
#2: Journal: Embo J. / Year: 1997
Title: The 1.25 A Crystal Structure of Sepiapterin Reductase Reveals its Binding Mode to Pterins and Brain Neurotransmitters
Authors: Auerbach, G. / Herrmann, A. / Gutlich, M. / Fischer, M. / Jacob, U. / Bacher, A. / Huber, R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Active Site Topology and Reaction Mechanism of GTP Cyclohydrolase I
Authors: Nar, H. / Huber, R. / Auerbach, G. / Fischer, M. / Hosl, C. / Ritz, H. / Bracher, A. / Meining, W. / Eberhardt, S. / Bacher, A.
#4: Journal: Structure / Year: 1995
Title: Atomic Structure of GTP Cyclohydrolase I
Authors: Nar, H. / Huber, R. / Meining, W. / Schmid, C. / Weinkauf, S. / Bacher, A.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Advisory / Database references / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
L: GTP CYCLOHYDROLASE I
M: GTP CYCLOHYDROLASE I
N: GTP CYCLOHYDROLASE I
O: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,08330
Polymers370,23615
Non-polymers7,84815
Water17,565975
1
A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
hetero molecules

A: GTP CYCLOHYDROLASE I
B: GTP CYCLOHYDROLASE I
C: GTP CYCLOHYDROLASE I
D: GTP CYCLOHYDROLASE I
E: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,05620
Polymers246,82410
Non-polymers5,23210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
2
F: GTP CYCLOHYDROLASE I
G: GTP CYCLOHYDROLASE I
H: GTP CYCLOHYDROLASE I
I: GTP CYCLOHYDROLASE I
J: GTP CYCLOHYDROLASE I
hetero molecules

K: GTP CYCLOHYDROLASE I
L: GTP CYCLOHYDROLASE I
M: GTP CYCLOHYDROLASE I
N: GTP CYCLOHYDROLASE I
O: GTP CYCLOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,05620
Polymers246,82410
Non-polymers5,23210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area61020 Å2
ΔGint-171 kcal/mol
Surface area75110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)314.950, 219.140, 131.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.349571, 0.924563, -0.151603), (-0.923599, 0.312885, -0.221514), (-0.15737, 0.217455, 0.9633)57.71806, 189.51826, 14.39037
2given(-0.70673, 0.579892, -0.405288), (-0.578697, -0.803373, -0.140362), (-0.406993, 0.135341, 0.903349)250.82587, 192.52682, 60.09977
3given(-0.719054, -0.561461, -0.40954), (0.561517, -0.816602, 0.133637), (-0.409464, -0.133872, 0.902451)314.2522, 4.82466, 74.97793
4given(0.340781, -0.926725, -0.158269), (0.926971, 0.303131, 0.22099), (-0.15682, -0.22202, 0.962348)158.80249, -115.81689, 37.93861
5given(0.282811, -0.95916, 0.005427), (0.855008, 0.254658, 0.451787), (-0.434718, -0.12313, 0.892109)107.67764, -130.55487, 138.53059
6given(0.983514, -0.034292, 0.177551), (-0.011365, 0.968191, 0.249953), (-0.180474, -0.24785, 0.95184)-58.00532, -25.96692, 103.29652
7given(0.335597, 0.941654, 0.025746), (-0.941799, 0.334824, 0.030138), (0.01976, -0.034362, 0.999214)-3.41777, 161.90179, 58.71762
8given(-0.75359, 0.613579, -0.235848), (-0.646881, -0.755982, 0.100185), (-0.116825, 0.228063, 0.966612)194.12193, 171.65503, 67.1991
9given(-0.79249, -0.556177, -0.250255), (0.456886, -0.81321, 0.360478), (-0.403999, 0.171337, 0.89857)263.6586, -7.46107, 117.72875
10given(-0.985061, -0.024073, -0.170518), (-0.018648, -0.969448, 0.244587), (-0.171196, 0.244113, 0.954516)420.22571, 124.00291, 21.08544
11given(-0.297583, -0.95459, -0.014186), (0.848758, -0.271336, 0.453857), (-0.437097, 0.12302, 0.890961)356.91144, -56.7951, 71.57045
12given(0.78095, -0.576543, 0.240241), (0.475187, 0.798059, 0.370539), (-0.405359, -0.175213, 0.89721)158.52103, -52.8659, 82.46189
13given(0.761441, 0.603507, 0.236616), (-0.637668, 0.762985, 0.105993), (-0.116567, -0.23159, 0.965804)98.2326, 132.98172, 37.72618
14given(-0.327668, 0.944628, -0.017639), (-0.944645, -0.32723, 0.0238), (0.016711, 0.024461, 0.999561)259.58069, 242.57234, 1.95584

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Components

#1: Protein
GTP CYCLOHYDROLASE I


Mass: 24682.381 Da / Num. of mol.: 15 / Mutation: H112S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: HOMOLOGOUS EXPRESSION / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6T5, GTP cyclohydrolase I
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 975 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium MES1reservoir
20.2 Msodium acetate1reservoir
33 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 238566 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.5 % / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 661363

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
MOSFLMdata reduction
X-PLOR3.8phasing
RefinementResolution: 2.1→8 Å / σ(F): 0 /
Rfactor% reflection
Rfree0.246 5 %
Rwork0.2 -
obs0.2 90.4 %
Displacement parametersBiso mean: 39.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27375 0 35 975 28385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 27375 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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