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- PDB-1a48: SAICAR SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1a48
TitleSAICAR SYNTHASE
ComponentsPHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
KeywordsATP BINDING PROTEIN / PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYNTHASE / PURINE BIOSYNTHESIS
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsLevdikov, V.M. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K.S.
Citation
Journal: Structure / Year: 1998
Title: The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
Authors: Levdikov, V.M. / Barynin, V.V. / Grebenko, A.I. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K.S.
#1: Journal: Biokhimiia / Year: 1992
Title: [Substrate Specificity of Phosphoribosyl-Aminoimidazole-Succinocarboxyamide Synthetase (Saicar-Synthetase) from Saccharomyces Cerevisiae Yeast] (Russian)
Authors: Alenin, V.V. / Ostanin, K.V. / Kostikova, T.R. / Domkin, V.D. / Zubova, V.A. / Smirnov, M.N.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Investigation of Phosphoribosylaminoimidazolesuccinocarboxamide Synthase from the Yeast Saccharomyces Cerevisiae
Authors: Grebenko, A.I. / Levdikov, V.M. / Barynin, V.V. / Melik-Adamyan, W.R. / Myasnikov, A.N.
#3: Journal: Prog.Nucleic Acid Res.Mol.Biol. / Year: 1992
Title: De Novo Purine Nucleotide Biosynthesis
Authors: Zalkin, H. / Dixon, J.E.
#4: Journal: Gene / Year: 1991
Title: The Saccharomyces Cerevisiae Ade1 Gene: Structure, Overexpression and Possible Regulation by General Amino Acid Control
Authors: Myasnikov, A.N. / Sasnauskas, K.V. / Janulaitis, A.A. / Smirnov, M.N.
#5: Journal: Biokhimiia / Year: 1989
Title: [Isolation and Properties of Phosphoribosyl-Aminoimidazole-Succinocarboxyamide-Synthetase from Saccharomyces Cerevisiae Yeasts] (Russian)
Authors: Ostanin, K.V. / Alenin, V.V. / Domkin, V.D. / Smirnov, M.N.
#6: Journal: Bioorg.Khim. / Year: 1986
Title: [Nucleotide Sequence of the Ade 1 Gene of the Yeast Saccharomyces Cerevisiae] (Russian)
Authors: Miasnikov, A.N. / Plavnik, Iu.A. / Sasnauskas, K.V. / Gedminene, G.K. / Ianulaitis, A.A.
History
DepositionFeb 12, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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: PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7373
Polymers34,5451
Non-polymers1922
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.600, 63.700, 81.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE / SAICAR SYNTHETASE


Mass: 34545.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: GRF18
References: UniProt: P27616, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-15 mg/mlprotein1drop
250 mMTris-HCl1drop
340 mMaspartic acid1drop
41.0-1.25 Mammonium sulfate1drop
550 mMTris-HCl1reservoir
62.25 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1991 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 24879 / % possible obs: 97 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→10 Å / σ(F): 0
Details: THE LAST CYCLES OF REFINEMENT INCLUDED THE PARTIAL CONTRIBUTION FROM HYDROGEN ATOMS PLACED AT THEIR IDEALISED POSITIONS WHICH RESULTED IN IMPROVEMENT OF THE R FACTOR BY ABOUT 0.010.
RfactorNum. reflection% reflection
obs0.153 24879 97 %
all-24879 -
Displacement parametersBiso mean: 23.2 Å2
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 13 319 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1792
X-RAY DIFFRACTIONp_mcangle_it3.2973
X-RAY DIFFRACTIONp_scbond_it5.4443
X-RAY DIFFRACTIONp_scangle_it8.274
X-RAY DIFFRACTIONp_plane_restr0.0170.02
X-RAY DIFFRACTIONp_chiral_restr0.2130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2730.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2420.3
X-RAY DIFFRACTIONp_planar_tor3.1193
X-RAY DIFFRACTIONp_staggered_tor20.1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.7920
X-RAY DIFFRACTIONp_special_tor

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