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- PDB-2jbv: Crystal structure of choline oxidase reveals insights into the ca... -

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Basic information

Entry
Database: PDB / ID: 2jbv
TitleCrystal structure of choline oxidase reveals insights into the catalytic mechanism
ComponentsCHOLINE OXIDASE
KeywordsOXIDOREDUCTASE / ALCOHOL OXIDATION / FLAVOENYZME OXIDASE / COVALENTLY LINKED FAD / ARTHROBACTER GLOBIFORMIS / C4A-ADDUCT / FLAVOPROTEIN / GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE ENZYME SUPERFAMILY
Function / homology
Function and homology information


choline oxidase / choline:oxygen 1-oxidoreductase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding
Similarity search - Function
Arc Repressor Mutant - #110 / Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Arc Repressor Mutant / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase ...Arc Repressor Mutant - #110 / Glucose Oxidase; domain 2 / Glucose Oxidase, domain 2 / Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Arc Repressor Mutant / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FAO / Choline oxidase
Similarity search - Component
Biological speciesARTHROBACTER GLOBIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLountos, G.T. / Fan, F. / Gadda, G. / Orville, A.M.
Citation
Journal: Biochemistry / Year: 2008
Title: Role of Glu312 in Binding and Positioning of the Substrate for the Hydride Transfer Reaction in Choline Oxidase.
Authors: Quaye, O. / Lountos, G.T. / Fan, F. / Orville, A.M. / Gadda, G.
#1: Journal: Arch.Biochem.Biophys. / Year: 2004
Title: Cloning, Sequence Analysis, and Purification of Choline Oxidase from Arthrobacter Globiformis: A Bacterial Enzyme Involved in Osmotic Stress Tolerance
Authors: Fan, F. / Ghanem, M. / Gadda, G.
#2: Journal: Biochim.Biophys.Acta / Year: 2003
Title: Kinetic Mechanism of Choline Oxidase from Arthrobacter Globiformis
Authors: Gadda, G.
#3: Journal: Arch.Biochem.Biophys. / Year: 2004
Title: The Trimethylammonium Headgroup of Choline is a Major Determinant for Substrate Binding and Specificity in Choline Oxidase
Authors: Gadda, G. / Powell, N.L. / Menon, P.
#4: Journal: J.Am.Chem.Soc. / Year: 2005
Title: On the Catalytic Mechanism of Choline Oxidase
Authors: Fan, F. / Gadda, G.
#5: Journal: Biochemistry / Year: 2005
Title: On the Catalytic Role of the Conserved Active Site Residue His466 of Choline Oxidase
Authors: Ghanem, M. / Gadda, G.
#6: Journal: Biochemistry / Year: 2006
Title: Effects of Reversing the Protein Positive Charge in the Proximity of the Flavin N(1) Locus of Choline Oxidase
Authors: Ghanem, M. / Gadda, G.
History
DepositionDec 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLINE OXIDASE
B: CHOLINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,53310
Polymers119,7982
Non-polymers1,7358
Water17,457969
1
A: CHOLINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7665
Polymers59,8991
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CHOLINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7665
Polymers59,8991
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.355, 84.355, 343.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CHOLINE OXIDASE


Mass: 59898.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT LINKAGE BETWEEN C8M ATOM OF FAO AND NE2 ATOM OF HIS99 OF CHOLINE OXIDASE
Source: (gene. exp.) ARTHROBACTER GLOBIFORMIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: Q7X2H8, choline oxidase
#2: Chemical ChemComp-FAO / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(4aS,10aR)-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate


Mass: 789.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N9O15P2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growTemperature: 296 K / pH: 8.5
Details: 4.9 MG/ML CHOLINE OXIDASE, 100 MM BIS TRIS PROPANE PH 8.5, 1.2 M AMMONIUM SULFATE, 10% V/V DMSO, 23 C CRYSTALS WERE CRYOPROTECTED BY SOAKING FOR 2 MIN IN 3.4 M SODIUM MALONATE PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→1.91 Å / Num. obs: 97546 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 63.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CF3

1cf3


Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.752 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 528-546 WERE NOT LOCATED IN THE EXPERIMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4894 5 %RANDOM
Rwork0.169 ---
obs0.171 92403 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8162 0 118 969 9249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0218493
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.96711576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66451055
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32123.547406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.075151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7571577
X-RAY DIFFRACTIONr_chiral_restr0.1120.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.24219
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25682
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2932
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9331.55398
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34628495
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.31533487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6554.53081
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: 1.86→1.91 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 223
Rwork0.23 4472

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