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- PDB-1of6: crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-hep... -

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Basic information

Entry
Database: PDB / ID: 1of6
Titlecrystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae complexed with tyrosine and manganese
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE, TYROSINE-INHIBITED
KeywordsLYASE / BETA-ALPHA-BARREL / SYNTHASE / ALDOLASE / SYNTHETASE
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
D-TYROSINE / : / Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / Schneider, T.R.
Citation
Journal: To be Published
Title: Crystal Structure of the Double Complex of the Tyrosine Sensitive Dahp Synthase from Yeast
Authors: Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / 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 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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_asym_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_asym_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 SHEETS PRESENTED AS "AB", "BA","CB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP SHEETS PRESENTED AS "AB", "BA","CB" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS THIS IS REPRESENTED BY 9-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA", "EB","FA","GB", "HA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS 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)320,26524
Polymers318,3768
Non-polymers1,88916
Water12,016667
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)80,0666
Polymers79,5942
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-28.4 kcal/mol
Surface area24300 Å2
MethodPISA
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)80,0666
Polymers79,5942
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-33.1 kcal/mol
Surface area24760 Å2
MethodPISA
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)80,0666
Polymers79,5942
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-33.3 kcal/mol
Surface area24290 Å2
MethodPISA
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)80,0666
Polymers79,5942
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-31.1 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.129, 94.696, 104.843
Angle α, β, γ (deg.)64.71, 85.51, 75.61
Int Tables number1
Space group name H-MP1
DetailsTHE 8 MOLECULES CONTAINED IN THE ASSYMETRIC UNIT AREARRANGED IN TWO TETRAMERS (DIMER OF DIMERS) WITH APPROXIMATE222 POINT SYMMETRY. THE TETRAMERS HAVE VERY SIMILARWITH THEIR CENTERS OF MASS BEING RELATED BY AORIENTATIONS,CRYSTALLOGRAPHIC TRANSLATION OF (0.5,0.5,0).

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Components

#1: Protein
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE, TYROSINE-INHIBITED / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE DAHP SYNTHETASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7- ...PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE DAHP SYNTHETASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / PHOSPHO-2-DEHYDRO- 3-DEOXYHEPTONATE ALDOLASE


Mass: 39797.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: RH1326 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32449, EC: 4.1.2.15
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Type: D-peptide linking / Mass: 181.189 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
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
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 2001 / 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: 2.05→20 Å / Num. obs: 407127 / % possible obs: 96.5 % / Observed criterion σ(I): 2.05 / Redundancy: 2.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.1
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.1 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MOLECULE A OF PDB-CODE 1HFB

1hfb


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4949 3.2 %RANDOM
Rwork0.195 ---
obs-151729 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 43.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20826 0 112 667 21605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02121227
X-RAY DIFFRACTIONr_bond_other_d00.0219411
X-RAY DIFFRACTIONr_angle_refined_deg1.9961.96128733
X-RAY DIFFRACTIONr_angle_other_deg3.888345224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93152748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.23315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223923
X-RAY DIFFRACTIONr_gen_planes_other0.010.023943
X-RAY DIFFRACTIONr_nbd_refined0.2180.24509
X-RAY DIFFRACTIONr_nbd_other0.2790.221440
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1140.211006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2757
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3720.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0641.513709
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.856221932
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.80737518
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4444.56801
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 1009
Rwork0.298 10347

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