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- PDB-1bgj: P-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED... -

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Basic information

Entry
Database: PDB / ID: 1bgj
TitleP-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED BY SER (C116S) AND HIS 162 REPLACED BY ARG (H162R), IN COMPLEX WITH FAD AND 4-HYDROXYBENZOIC ACID
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase [NADPH] activity / 4-hydroxybenzoate 3-monooxygenase activity / benzoate catabolic process via hydroxylation / FAD binding / flavin adenine dinucleotide binding
Similarity search - Function
4-hydroxybenzoate 3-monooxygenase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / P-HYDROXYBENZOIC ACID / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEppink, M.H.M. / Schreuder, H.A. / Van Berkel, W.J.H.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Interdomain binding of NADPH in p-hydroxybenzoate hydroxylase as suggested by kinetic, crystallographic and modeling studies of histidine 162 and arginine 269 variants.
Authors: Eppink, M.H. / Schreuder, H.A. / van Berkel, W.J.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: Lys42 and Ser42 Variants of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens Reveal that Arg42 is Essential for Nadph Binding
Authors: Eppink, M.H. / Schreuder, H.A. / Van Berkel, W.J.
#2: Journal: Protein Sci. / Year: 1994
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase Reconstituted with the Modified Fad Present in Alcohol Oxidase from Methylotrophic Yeasts: Evidence for an Arabinoflavin
Authors: Van Berkel, W.J. / Eppink, M.H. / Schreuder, H.A.
#3: Journal: Biochemistry / Year: 1994
Title: Crystal Structures of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate, 2,4-Dihydroxybenzoate, and 2-Hydroxy-4-Aminobenzoate and of the Tyr222Ala Mutant Complexed with 2- ...Title: Crystal Structures of Wild-Type P-Hydroxybenzoate Hydroxylase Complexed with 4-Aminobenzoate, 2,4-Dihydroxybenzoate, and 2-Hydroxy-4-Aminobenzoate and of the Tyr222Ala Mutant Complexed with 2-Hydroxy-4-Aminobenzoate. Evidence for a Proton Channel and a New Binding Mode of the Flavin Ring
Authors: Schreuder, H.A. / Mattevi, A. / Obmolova, G. / Kalk, K.H. / Hol, W.G. / Van Der Bolt, F.J. / Van Berkel, W.J.
#4: Journal: Proteins / Year: 1992
Title: Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined at 2.3 A Resolution
Authors: Schreuder, H.A. / Van Der Laan, J.M. / Swarte, M.B. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#5: Journal: FEBS Lett. / Year: 1990
Title: Engineering of Microheterogeneity-Resistant P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Eschrich, K. / Van Berkel, W.J. / Westphal, A.H. / De Kok, A. / Mattevi, A. / Obmolova, G. / Kalk, K.H. / Hol, W.G.
#6: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 A Resolution. Analysis of the Enzyme-Substrate and Enzyme-Product Complexes
Authors: Schreuder, H.A. / Prick, P.A. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G. / Drenth, J.
#7: Journal: Biochemistry / Year: 1989
Title: The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces Fad in the Active Site of P-Hydroxybenzoate Hydroxylase. An X-Ray Crystallographic Investigation
Authors: Van Der Laan, J.M. / Schreuder, H.A. / Swarte, M.B. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#8: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase Complexed with its Reaction Product 3,4-Dihydroxybenzoate
Authors: Schreuder, H.A. / Van Der Laan, J.M. / Hol, W.G. / Drenth, J.
#9: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase
Authors: Wierenga, R.K. / De Jong, R.J. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#10: Journal: J.Biol.Chem. / Year: 1975
Title: Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Drenth, J. / Hol, W.G. / Wierenga, R.K.
History
DepositionMay 29, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3073
Polymers44,3841
Non-polymers9242
Water3,927218
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6146
Polymers88,7672
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6340 Å2
ΔGint-32 kcal/mol
Surface area30820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.800, 146.000, 88.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein P-HYDROXYBENZOATE HYDROXYLASE


Mass: 44383.555 Da / Num. of mol.: 1 / Mutation: C116S, H162R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: POBA / Plasmid: PUC9 / Gene (production host): POBA / Production host: Escherichia coli (E. coli) / Strain (production host): TG2
References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7
Details: 39% AMMONIUMSULFATE, 100 MM SODIUM PHOSPHATE, 0.04 MM FAD, 0.15 MM EDTA, 30 MM SODIUM SULFITE, 1 MM P-HYDROXYBENZOATE, pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlenzyme1drop
2100 mMpotassium phosphate1drop
340 %satammonium sulfate1reservoir
40.04 mMFAD1reservoir
50.15 mMEDTA1reservoir
62 mMPOHB1reservoir
730 mMsodium sulfite1reservoir
8100 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→8 Å / Num. obs: 6695 / % possible obs: 72.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Rsym value: 0.067
Reflection
*PLUS
Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PBE

1pbe


Resolution: 3→8 Å /
RfactorNum. reflection
Rwork0.128 -
obs0.128 6695
Displacement parametersBiso mean: 26.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 63 218 3380
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.74
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2FAD.PARFAD.TOP
X-RAY DIFFRACTION3WAT.PARPHB.TOP
X-RAY DIFFRACTION4WAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.74

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