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- PDB-3ggo: Crystal structure of prephenate dehydrogenase from A. aeolicus wi... -

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Basic information

Entry
Database: PDB / ID: 3ggo
TitleCrystal structure of prephenate dehydrogenase from A. aeolicus with HPP and NADH
ComponentsPrephenate dehydrogenase
KeywordsOXIDOREDUCTASE / Tyra / HPP / NADH / alpha-beta
Function / homology
Function and homology information


prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / NAD+ binding
Similarity search - Function
Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, dimerization domain / 6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Prephenate dehydrogenase, dimerization domain / Prephenate dehydrogenase, dimerization domain / 6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-(4-HYDROXY-PHENYL)PYRUVIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Prephenate dehydrogenase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSun, W. / Shahinas, D. / Christendat, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Crystal Structure of Aquifex aeolicus Prephenate Dehydrogenase Reveals the Mode of Tyrosine Inhibition.
Authors: Sun, W. / Shahinas, D. / Bonvin, J. / Hou, W. / Kimber, M.S. / Turnbull, J. / Christendat, D.
History
DepositionMar 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / 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: Prephenate dehydrogenase
B: Prephenate dehydrogenase
C: Prephenate dehydrogenase
D: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,07710
Polymers141,0554
Non-polymers3,0226
Water4,630257
1
A: Prephenate dehydrogenase
C: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0395
Polymers70,5282
Non-polymers1,5113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-81 kcal/mol
Surface area22910 Å2
MethodPISA
2
B: Prephenate dehydrogenase
D: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0395
Polymers70,5282
Non-polymers1,5113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-83 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.496, 92.481, 164.083
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
Prephenate dehydrogenase /


Mass: 35263.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1755, tyrA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: O67636
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-ENO / 3-(4-HYDROXY-PHENYL)PYRUVIC ACID / HPP / 4-Hydroxyphenylpyruvic acid


Mass: 180.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100mM HEPES, 48% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→46.24 Å / Num. obs: 66487 / % possible obs: 96.4 % / Observed criterion σ(I): 1.3 / Redundancy: 9.1 % / Rsym value: 0.048 / Net I/σ(I): 47.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.52 / % possible all: 67.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2G5C

2g5c


Resolution: 2.15→46.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.791 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2030 3.1 %RANDOM
Rwork0.21755 ---
obs0.2189 64377 96.29 %-
all-66783 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å2-0 Å2
2---0.18 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8922 0 202 257 9381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229315
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8042.00912569
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49451126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64424.263373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.114151733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8581543
X-RAY DIFFRACTIONr_chiral_restr0.1260.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216759
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.24548
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26392
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8831.55593
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50229055
X-RAY DIFFRACTIONr_scbond_it2.6733722
X-RAY DIFFRACTIONr_scangle_it3.9364.53514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 112 -
Rwork0.338 3401 -
obs--69.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4259-0.84172.51093.4873-1.23664.5084-0.0493-0.84210.0495-0.0795-0.10880.5367-0.0636-0.6260.1580.00020.0418-0.10280.253-0.28310.387223.864-89.61639.616
24.13891.24-1.54795.1656-0.73862.19440.010.25420.7825-0.32550.1358-0.501-0.2723-0.1178-0.1458-0.02660.05610.05990.04530.04690.347729.76221.547-14.227
33.8121-1.09891.19653.6283-0.49932-0.04310.02460.3447-0.1225-0.14150.0407-0.26730.01980.18460.0776-0.0166-0.1520.0895-0.01950.111313.356-33.81827.389
46.1236-1.79571.20184.6211-0.73053.06060.53680.7760.2013-0.4676-0.16580.5231-0.0236-0.4025-0.37110.2220.16960.20830.26060.30460.480413.424-34.672-15.928
51.4894-1.14590.18525.78780.411.28980.25070.3237-0.1426-0.3352-0.1646-0.3550.10910.3411-0.0862-0.00210.0897-0.09110.2726-0.05410.105829.188-61.35424.472
62.93681.1417-1.11966.5043-0.77321.9441-0.4082-0.3393-0.34880.45160.1454-0.28170.2598-0.02580.26280.04190.11770.08890.16070.06150.124221.037-6.048-1.823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 205
2X-RAY DIFFRACTION2B28 - 205
3X-RAY DIFFRACTION3C25 - 205
4X-RAY DIFFRACTION4D27 - 205
5X-RAY DIFFRACTION5A206 - 310
6X-RAY DIFFRACTION5C206 - 305
7X-RAY DIFFRACTION6B206 - 309
8X-RAY DIFFRACTION6D206 - 308

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