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- PDB-1og0: CRYSTAL STRUCTURE OF THE MUTANT G226S OF THE TYROSINE-REGULATED 3... -

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Entry
Database: PDB / ID: 1og0
TitleCRYSTAL STRUCTURE OF THE MUTANT G226S OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
KeywordsLYASE / BETA-ALPHA-BARREL
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleus / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKoenig, V. / Pfeil, A. / Heinrich, G. / Braus, G.H. / Schneider, T.R.
Citation
Journal: To be Published
Title: Crystal Structure of the Mutant G226S of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate -7-Phosphate Synthase from Saccharomyces Cerevisiae Complexed with Phenylalanine and Manganese
Authors: Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G.H. / Schneider, T.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Evolution of Feedback-Inhibited Beta /Alpha Barrel Isoenzymes by Gene Duplication and a Single Mutation.
Authors: Hartmann, M. / Schneider, T.R. / Pfeil, A. / Heinrich, G. / Lipscomb, W.N. / Braus, G.H.
History
DepositionApr 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 19, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list ..._diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
E: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
F: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
G: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
H: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,21223
Polymers318,6178
Non-polymers1,59615
Water1,76598
1
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9295
Polymers79,6542
Non-polymers2753
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0946
Polymers79,6542
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
F: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0946
Polymers79,6542
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
H: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0946
Polymers79,6542
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
F: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
G: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
H: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,18912
Polymers159,3084
Non-polymers8818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-93.7 kcal/mol
Surface area46360 Å2
MethodPISA
6
A: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
B: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
C: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
D: Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,02411
Polymers159,3084
Non-polymers7157
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14150 Å2
ΔGint-79.98 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.154, 93.971, 104.843
Angle α, β, γ (deg.)65.39, 85.77, 75.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 39827.082 Da / Num. of mol.: 8 / Mutation: G226S
Source method: isolated from a genetically manipulated source
Details: LIGANDS PHENYLALANINE ION, MANGANESE
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARO4, YBR249C, YBR1701 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32449, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = ...CATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = PHOSPHOENOLPYRUVATE + D-ERYTHROSE 4- PHOSPHATE + 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8463 / Wavelength: 0.8463 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2002 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8463 Å / Relative weight: 1
ReflectionResolution: 2.7→37 Å / Num. obs: 155910 / % possible obs: 91.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.8
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.5 / % possible all: 78.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFB MOLECULE A

1hfb


Resolution: 2.7→29.83 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3373 5.2 %RANDOM
Rwork0.213 ---
obs0.213 72685 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.0212 Å2 / ksol: 0.315139 e/Å3
Displacement parametersBiso mean: 50.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.59 Å2-7.67 Å2-0.87 Å2
2--4.16 Å22.68 Å2
3----10.75 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20640 0 92 98 20830
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it2.462
X-RAY DIFFRACTIONc_scangle_it3.682.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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