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Yorodumi- PDB-1pbd: CRYSTAL STRUCTURES OF WILD-TYPE P-HYDROXYBENZOATE HYDROXYLASE COM... -
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-Basic information
Entry | Database: PDB / ID: 1pbd | ||||||
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Title | CRYSTAL STRUCTURES OF WILD-TYPE P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-AMINOBENZOATE, 2,4-DIHYDROXYBENZOATE AND 2-HYDROXY-4-AMINOBENZOATE AND OF THE TRY222ALA MUTANT, COMPLEXED WITH 2-HYDROXY-4-AMINOBENZOATE. EVIDENCE FOR A PROTON CHANNEL AND A NEW BINDING MODE OF THE FLAVIN RING | ||||||
Components | P-HYDROXYBENZOATE HYDROXYLASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Schreuder, H.A. / Mattevi, A. / Hol, W.G.J. | ||||||
Citation | 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. #1: Journal: Proteins / Year: 1992 Title: Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined at 2.3 Angstroms Resolution Authors: Schreuder, H.A. / Van Der Laan, J.M. / Swarte, M.B.A. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #2: Journal: Eur.J.Biochem. / Year: 1989 Title: The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase Authors: Van Der Laan, J.M. / Swarte, M.B.A. / Groendijk, H. / Hol, W.G.J. / Drenth, J. #3: 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.A. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G.J. / Drenth, J. #4: Journal: Biochemistry / Year: 1989 Title: Analysis of the Active Site of the Flavoprotein P-Hydroxybenzoate Hydroxylase and Some Ideas with Respect to its Reaction Mechanism Authors: Schreuder, H.A. / Hol, W.G.J. / Drenth, J. #5: Journal: J.Mol.Biol. / Year: 1989 Title: Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution. Analysis of the Enzyme-Substrate and Enzyme-Product Complexes Authors: Schreuder, H.A. / Prick, P.A.J. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G.J. / Drenth, J. #6: Journal: J.Biol.Chem. / Year: 1988 Title: Molecular Modeling Reveals the Possible Importance of a Carbonyl Oxygen Binding Pocket for the Catalytic Mechanism of P-Hydroxybenzoate Hydroxylase Authors: Schreuder, H.A. / Hol, W.G.J. / 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.J. / Drenth, J. #8: Journal: J.Mol.Biol. / Year: 1983 Title: Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase Authors: Wierenga, R.K. / Drenth, J. / Schulz, G.E. #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.J. / 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.J. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pbd.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pbd.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/1pbd ftp://data.pdbj.org/pub/pdb/validation_reports/pb/1pbd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 275 |
-Components
#1: Protein | Mass: 44364.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-PAB / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.35 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: free interface liquid-liquid diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 14434 / % possible obs: 67.8 % / Rmerge(I) obs: 0.047 |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.156 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.5 |