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- PDB-6y9c: The structure of a quaternary ammonium Rieske monooxygenase revea... -

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Basic information

Entry
Database: PDB / ID: 6y9c
TitleThe structure of a quaternary ammonium Rieske monooxygenase reveals insights into carnitine oxidation by gut microbiota and inter-subunit electron transfer
ComponentsCarnitine monooxygenase oxygenase subunit
KeywordsOXIDOREDUCTASE / Apo / Rieske / Iron-Sulphur Cluster
Function / homology
Function and homology information


carnitine monooxygenase / carnitine metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Carnitine monooxygenase oxygenase subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
CARNITINE / : / FE2/S2 (INORGANIC) CLUSTER / THIOCYANATE ION / Carnitine monooxygenase oxygenase subunit
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsQuareshy, M. / Shanmugam, M. / Bugg, T.D. / Cameron, A. / Chen, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2016-307 United Kingdom
CitationJournal: Febs J. / Year: 2023
Title: Characterisation of an unusual cysteine pair in the Rieske carnitine monooxygenase CntA catalytic site.
Authors: Quareshy, M. / Shanmugam, M. / Cameron, A.D. / Bugg, T.D.H. / Chen, Y.
History
DepositionMar 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2005
Polymers44,7481
Non-polymers4524
Water1,67593
1
A: Carnitine monooxygenase oxygenase subunit
hetero molecules

A: Carnitine monooxygenase oxygenase subunit
hetero molecules

A: Carnitine monooxygenase oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,60015
Polymers134,2443
Non-polymers1,35612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11100 Å2
ΔGint-123 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.242, 91.242, 87.366
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carnitine monooxygenase oxygenase subunit / Carnitine monooxygenase alpha subunit


Mass: 44748.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, ...Gene: antA_2, antA_1, antA_3, A7M79_02670, A7M90_13970, ABUW_3074, B4R90_07590, B9X95_06095, BGC29_09330, C2U32_18540, C3415_14505, CBI29_00874, CHQ89_11265, CPI82_11190, CSB70_0522, DLI75_01970, DOL94_04925, DVA79_16365, E2533_13315, E2536_16135, E5294_15630, E5979_13670, EA685_07170, EA686_01565, EA706_03020, EA722_03860, EA746_003300, EWO92_12480, EWO96_16565, EWP49_15025, FD887_09300, FD913_14110, FJU36_15000, FJU42_16200, FJU76_14830, FJU79_08840, FJU87_10695, FJV14_20515, LV38_02893, NCTC13305_01609, SAMEA104305283_02985, SAMEA104305351_01970
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A059ZPP5, carnitine monooxygenase

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-152 / CARNITINE / (3-CARBOXY-2-(R)-HYDROXY-PROPYL)-TRIMETHYL-AMMONIUM


Mass: 162.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.57 % / Description: Red Hexagonal Crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 10mM HEPES, 20% PEG3350, 0.2M NaSCN, 0.5mM TCEP / PH range: 7.0 - 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.8→38.23 Å / Num. obs: 38296 / % possible obs: 94.65 % / Redundancy: 11.8 % / Biso Wilson estimate: 18.71 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1739 / Rpim(I) all: 0.0515 / Rrim(I) all: 0.1816 / Net I/σ(I): 4.15
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 0.36 / Num. unique obs: 3808 / CC1/2: 0.885 / CC star: 0.969 / Rpim(I) all: 0.499 / Rrim(I) all: 1.442

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VCP

3vcp


Resolution: 1.8→38.23 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2923 3344 4.78 %
Rwork0.2461 66639 -
obs0.2483 36236 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.74 Å2 / Biso mean: 41.3487 Å2 / Biso min: 14.1 Å2
Refinement stepCycle: final / Resolution: 1.8→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 34 93 3088
Biso mean--43.32 33.15 -
Num. residues----365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8001-1.82580.51151380.405287594
1.8258-1.8530.46041390.3735281495
1.853-1.8820.36931380.3911281895
1.882-1.91280.5228600.5307143047
1.9128-1.94580.51071430.4125219274
1.9458-1.98120.36971420.3128285196
1.9812-2.01930.3441390.3017287497
2.0193-2.06050.3191480.2987289798
2.0605-2.10530.32251710.2925297498
2.1053-2.15430.33961050.2626293999
2.1543-2.20820.34171560.26942978100
2.2082-2.26780.5217670.4016126542
2.2678-2.33460.28961840.22952993100
2.3346-2.40990.2491640.22632965100
2.4099-2.4960.31651240.23443015100
2.496-2.59590.349990.24553045100
2.5959-2.71410.27421460.24892957100
2.7141-2.85710.34551760.2562962100
2.8571-3.0360.27441540.23772986100
3.036-3.27030.24481410.23523003100
3.2703-3.59920.24751470.22292989100
3.5992-4.11950.35451280.2301292198
4.1195-5.18810.18151390.1556299299
5.1881-38.230.2131960.1869290498
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)
11.3121-0.0320.03181.5610.01430.5124-0.0377-0.12490.21810.0162-0.0286-0.4416-0.0663-0.02550.0420.1548-0.018-0.02370.1843-0.00340.4772-23.9398-12.0085-0.7249
20.76610.03460.17141.7289-1.64981.6806-0.13960.266-0.5309-0.95230.1351-0.6880.76020.25580.05960.3440.03010.09380.314-0.01531.0496-9.1619-32.621-9.4665
31.18780.0579-0.04181.6513-0.01580.62550.0196-0.0689-0.3662-0.23160.0035-0.72090.0858-0.0292-0.0950.2009-0.01120.00130.15690.00580.4376-20.3268-31.2138-6.2105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 203 )A3 - 203
2X-RAY DIFFRACTION2chain 'A' and (resid 204 through 276 )A204 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 371 )A277 - 371

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