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- PDB-1a9c: GTP CYCLOHYDROLASE I (C110S MUTANT) IN COMPLEX WITH GTP -

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Basic information

Entry
Database: PDB / ID: 1a9c
TitleGTP CYCLOHYDROLASE I (C110S MUTANT) IN COMPLEX WITH GTP
ComponentsGTP CYCLOHYDROLASE I
KeywordsHYDROLASE / GTP / PURINE HYDROLYSIS / PTERINE SYNTHESIS / TETRAHYDROBIOPTERIN
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 / Resolution: 2.9 Å
AuthorsAuerbach, G. / Nar, H. / Bracher, A. / Bacher, A. / Huber, R.
Citation
Journal: To be Published
Title: GTP Cyclohydrolase I in Complex with GTP at 2.1 A Resolution
Authors: Auerbach, G. / Bracher, A. / Nar, H. / Fischer, M. / Hoesl, C. / Huber, R. / Bacher, A.
#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
DepositionApr 4, 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)378,60930
Polymers370,76115
Non-polymers7,84815
Water3,783210
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)252,40620
Polymers247,17410
Non-polymers5,23210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area62790 Å2
ΔGint-151.3 kcal/mol
Surface area73090 Å2
MethodPISA
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)252,40620
Polymers247,17410
Non-polymers5,23210
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area62960 Å2
ΔGint-151 kcal/mol
Surface area72950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)313.900, 226.800, 131.400
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(0.336097, 0.931189, -0.141159), (-0.931147, 0.306024, -0.19828), (-0.141438, 0.198081, 0.969927)58.54697, 190.24513, 12.49583
2given(-0.726712, 0.579137, -0.369445), (-0.578639, -0.805925, -0.125151), (-0.370224, 0.122827, 0.920786)251.74037, 192.69717, 54.17442
3given(-0.730029, -0.574697, -0.36984), (0.574068, -0.809299, 0.12442), (-0.370815, -0.121483, 0.920727)314.68262, 3.61025, 67.46434
4given(0.338093, -0.930553, -0.140588), (0.929786, 0.30717, 0.202839), (-0.145568, -0.199295, 0.969067)158.78624, -115.17979, 34.77695
5given(0.313561, -0.949326, 0.021435), (0.862188, 0.294093, 0.412482), (-0.397884, -0.110858, 0.910713)101.99724, -131.79814, 131.95389
6given(0.985705, 0.000525, 0.16848), (-0.038218, 0.974625, 0.220559), (-0.164089, -0.223845, 0.960712)-59.65208, -20.9794, 99.74176
7given(0.30959, 0.950636, 0.021097), (-0.950734, 0.309095, 0.023774), (0.01608, -0.027418, 0.999495)-0.03917, 164.76985, 59.50635
8given(-0.780478, 0.588421, -0.211222), (-0.615582, -0.782286, 0.095324), (-0.109145, 0.204423, 0.972779)198.15701, 168.86076, 67.4955
9given(-0.782432, -0.583052, -0.218748), (0.500003, -0.797582, 0.337432), (-0.37121, 0.154643, 0.915581)262.17328, -13.28954, 113.32336
10given(-0.986617, -0.000477, -0.163056), (-0.035627, -0.975204, 0.21842), (-0.159117, 0.221306, 0.962136)417.79761, 131.50827, 19.47031
11given(-0.315015, -0.948758, -0.024977), (0.860673, -0.296662, 0.413804), (-0.40001, 0.108857, 0.910023)359.21381, -52.21379, 65.1794
12given(0.778029, -0.590562, 0.214261), (0.508459, 0.792255, 0.337344), (-0.368972, -0.15352, 0.916674)160.36862, -53.35361, 74.23006
13given(0.782183, 0.585574, 0.212821), (-0.613531, 0.783383, 0.099448), (-0.108486, -0.208359, 0.972017)96.20692, 131.10434, 34.49833
14given(-0.306014, 0.951754, -0.02281), (-0.951948, -0.305592, 0.020223), (0.012276, 0.027903, 0.999535)254.87314, 245.73418, 1.89722

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Components

#1: Protein
GTP CYCLOHYDROLASE I


Mass: 24717.387 Da / Num. of mol.: 15 / Mutation: C110S
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.: 210 / 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: 3.16 Å3/Da / Density % sol: 61 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 6, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 86307 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.082

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
MOSFLMdata reduction
X-PLOR3.8phasing
RefinementResolution: 2.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 -5 %RANDOM
Rwork0.206 ---
obs0.206 82376 84.4 %-
Displacement parametersBiso mean: 32.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32055 0 35 255 32345
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.72
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

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