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- PDB-1qf4: DESIGN, SYNTHESIS, AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME BOUND... -

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Basic information

Entry
Database: PDB / ID: 1qf4
TitleDESIGN, SYNTHESIS, AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME BOUND BISUBSTRATE HYBRID INHIBITOR OF ADENYLOSUCCINATE SYNTHETASE
ComponentsPROTEIN (ADENYLOSUCCINATE SYNTHETASE)
KeywordsLIGASE / PURINE BIOSYNTHESIS / SYNTHETASE / GTP-BINDING / GTP-HYDROLYSING ENZYMES
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / nucleobase-containing small molecule interconversion / 'de novo' AMP biosynthetic process / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding ...adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / nucleobase-containing small molecule interconversion / 'de novo' AMP biosynthetic process / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding / magnesium ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / (C8-R)-HYDANTOCIDIN 5'-PHOSPHATE / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHanessian, S. / Lu, P.-P. / Sanceau, J.-Y. / Chemla, P. / Gohda, K. / Fonne-Pfister, R. / Prade, L. / Cowan-Jacob, S.W.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 1999
Title: An enzyme-bound bisubstrate hybrid inhibitor of adenylosuccinate synthetase
Authors: Hanessian, S. / Lu, P.P. / Sanceau, J.Y. / Chemla, P. / Gohda, K. / Fonne-Pfister, R. / Prade, L. / Cowan-Jacob, S.W.
#1: Journal: Biochemistry / Year: 1996
Title: Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin.
Authors: Poland, B.W. / Lee, S.F. / Subramanian, M.V. / Siehl, D.L. / Anderson, R.J. / Fromm, H.J. / Honzatko, R.B.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Refined crystal structures of unligated adenylosuccinate synthetase from Escherichia coli.
Authors: Silva, M.M. / Poland, B.W. / Hoffman, C.R. / Fromm, H.J. / Honzatko, R.B.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Crystal structure of adenylosuccinate synthetase from Escherichia coli. Evidence for convergent evolution of GTP-binding domains.
Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M. / Honzatko, R.B.
History
DepositionApr 6, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Aug 16, 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_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.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.value / _struct_conn.pdbx_dist_value / _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_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: PROTEIN (ADENYLOSUCCINATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2915
Polymers47,2701
Non-polymers1,0224
Water1,45981
1
A: PROTEIN (ADENYLOSUCCINATE SYNTHETASE)
hetero molecules

A: PROTEIN (ADENYLOSUCCINATE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,58310
Polymers94,5392
Non-polymers2,0448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area9760 Å2
ΔGint-79 kcal/mol
Surface area28030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.520, 81.520, 158.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (ADENYLOSUCCINATE SYNTHETASE) / E.C.6.3.4.4


Mass: 47269.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: A GIFT FROM DR. B. BACHURCE 4 (GENETIC CENTER, YALE UNIVERSITY)
Source: (natural) Escherichia coli (E. coli) / Strain: PUR A STRAIN H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase

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Non-polymers , 5 types, 85 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-RPD / (C8-R)-HYDANTOCIDIN 5'-PHOSPHATE / [8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL] PHOSPHATE


Mass: 459.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N3O13P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 416 DIVERGES FROM THE DNA SEQUENCE GIVEN IN PIR:A61592 AND IS GLYCINE IN THIS ENTRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mcacodylate11
20.2 Mmagnesium acetate11
316 %PEG600011

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. obs: 27564 / % possible obs: 88.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.086

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR98refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JUY

1juy


Resolution: 2.2→6 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -10 %RANDOM
Rwork0.194 ---
all-26333 --
obs-26333 95.3 %-
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 64 81 3466
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_deg1.341
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
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
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4

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