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- PDB-1cc4: PHE161 AND ARG166 VARIANTS OF P-HYDROXYBENZOATE HYDROXYLASE. IMPL... -

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Basic information

Entry
Database: PDB / ID: 1cc4
TitlePHE161 AND ARG166 VARIANTS OF P-HYDROXYBENZOATE HYDROXYLASE. IMPLICATIONS FOR NADPH RECOGNITION AND STRUCTURAL STABILITY.
ComponentsPROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
KeywordsOXIDOREDUCTASE / HYDROXYBENZOATE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase (NADPH) activity / 4-hydroxybenzoate 3-monooxygenase / 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 ...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: 2 Å
AuthorsEppink, M.H.M. / Bunthof, C. / Schreuder, H.A. / Van Berkel, W.J.H.
Citation
Journal: Febs Lett. / Year: 1999
Title: Phe161 and Arg166 variants of p-hydroxybenzoate hydroxylase. Implications for NADPH recognition and structural stability.
Authors: Eppink, M.H. / Bunthol, C. / Schreuder, H.A. / van Berkel, W.J.
#1: 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
#8: 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.
#9: 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
DepositionMar 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 12, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.6Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2123
Polymers44,2881
Non-polymers9242
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules

A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4246
Polymers88,5772
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6320 Å2
ΔGint-30 kcal/mol
Surface area30340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.700, 146.300, 88.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: Protein PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)


Mass: 44288.414 Da / Num. of mol.: 1 / Mutation: F161A, C116S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: TG2 / 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


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


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


Mass: 18.015 Da / Num. of mol.: 292 / 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: 53.04 %
Crystal growpH: 7 / Details: pH 7.0
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2NA3PO411
3NA2SO311
4EDTA11
5P-HYDROXYBENZOATE11
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Eppink, M.H.M., (1995) Eur. J. Biochem., 231, 157.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
2100 mMpotassium phosphate1drop
339 %satammonium sulfate1reservoir
40.04 mMFAD1reservoir
50.15 mMEDTA1reservoir
61 mM4-hydroxybenzoate1reservoir
760 mMsodium sulfite1reservoir
8100 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. all: 27343 / Num. obs: 27343 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 4.9 / Net I/σ(I): 12
Reflection
*PLUS
Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBE

1pbe


Resolution: 2→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.179 --
all-27343 -
obs-27343 94.4 %
Displacement parametersBiso mean: 27.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 63 292 3447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.43
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.75
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: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.75

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