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Basic information

Entry
Database: PDB / ID: 3ey9
TitleStructural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli
ComponentsPyruvate dehydrogenase [cytochrome]
KeywordsOXIDOREDUCTASE / Pyruvate oxidase / membrane-associated flavoprotein dehydrogenase / interactions with lipids / Cell membrane / FAD / Flavoprotein / Lipid-binding / Magnesium / Membrane / Thiamine pyrophosphate
Function / homology
Function and homology information


pyruvate dehydrogenase (quinone) / pyruvate dehydrogenase (quinone) activity / pyruvate catabolic process / pyruvate metabolic process / thiamine pyrophosphate binding / ubiquinone binding / flavin adenine dinucleotide binding / lipid binding / magnesium ion binding / protein-containing complex ...pyruvate dehydrogenase (quinone) / pyruvate dehydrogenase (quinone) activity / pyruvate catabolic process / pyruvate metabolic process / thiamine pyrophosphate binding / ubiquinone binding / flavin adenine dinucleotide binding / lipid binding / magnesium ion binding / protein-containing complex / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Pyruvate dehydrogenase [ubiquinone] PoxB-like / : / : / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain ...Pyruvate dehydrogenase [ubiquinone] PoxB-like / : / : / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / Pyruvate dehydrogenase [ubiquinone]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsNeumann, P. / Weidner, A. / Pech, A. / Stubbs, M.T. / Tittmann, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli.
Authors: Neumann, P. / Weidner, A. / Pech, A. / Stubbs, M.T. / Tittmann, K.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Other
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls_group / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase [cytochrome]
B: Pyruvate dehydrogenase [cytochrome]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,82910
Polymers124,1662
Non-polymers2,6628
Water00
1
A: Pyruvate dehydrogenase [cytochrome]
B: Pyruvate dehydrogenase [cytochrome]
hetero molecules

A: Pyruvate dehydrogenase [cytochrome]
B: Pyruvate dehydrogenase [cytochrome]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,65820
Polymers248,3334
Non-polymers5,32516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area32400 Å2
ΔGint-304 kcal/mol
Surface area69110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.370, 151.370, 153.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND ((RESID 5:464 OR RESID 482:566) AND (NAME CA OR NAME N OR NAME C OR NAME O))
21CHAIN B AND ((RESID 5:464 OR RESID 482:566) AND (NAME CA OR NAME N OR NAME C OR NAME O))
12CHAIN A AND (( RESID 5:37 OR RESID 39:65 OR...
22CHAIN B AND (( RESID 5:37 OR RESID 39:65 OR...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLYGLYAA5 - 4645 - 464
121LEULEUALAALAAA482 - 566482 - 566
211VALVALGLYGLYBB5 - 4645 - 464
221LEULEUALAALABB482 - 566482 - 566
112LYSLYSARGARGAA2 - 5722 - 572
212LYSLYSARGARGBB2 - 5722 - 572

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.102897, -0.894861, 0.434323), (-0.895944, -0.106292, -0.431261), (0.432084, -0.433504, -0.790808)74.377602, 74.499802, 0.060531
2given(-0.102819, -0.894927, 0.434205), (-0.896007, -0.10624, -0.431142), (0.431971, -0.43338, -0.790938)74.372498, 74.509399, 0.062524

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Components

#1: Protein Pyruvate dehydrogenase [cytochrome] / Pyruvate oxidase / POX / Pyruvate dehydrogenase / Alpha-peptide


Mass: 62083.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: poxB, b0871, JW0855 / Plasmid: pYYC102 / Production host: Escherichia coli (E. coli) / Strain (production host): ZK126 / References: UniProt: P07003, EC: 1.2.2.2
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 80mM potassium phosphate, 0-1% PEG 2000, 0.05-0.1% protamine sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54179 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 39657 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 72.85 Å2 / Rmerge(I) obs: 0.0073 / Rsym value: 0.0083 / Net I/σ(I): 25.07
Reflection shellResolution: 2.9→3 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.54 / Num. unique all: 3800 / Rsym value: 0.739 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.15 Å29.08 Å
Translation3.15 Å29.08 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1POW

1pow


Resolution: 2.9→29.97 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): 0 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1982 5 %
Rwork0.182 --
all0.183 39657 -
obs0.183 39635 98.79 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.039 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 242.2 Å2 / Biso mean: 80.719 Å2 / Biso min: 34.47 Å2
Baniso -1Baniso -2Baniso -3
1--12.843 Å2-0 Å20 Å2
2---12.843 Å2-0 Å2
3---25.685 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.354 Å
Luzzati d res low-2.9 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8684 0 170 0 8854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079038
X-RAY DIFFRACTIONf_angle_d1.12912272
X-RAY DIFFRACTIONf_chiral_restr0.0731368
X-RAY DIFFRACTIONf_plane_restr0.0051574
X-RAY DIFFRACTIONf_dihedral_angle_d19.353274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2180X-RAY DIFFRACTIONPOSITIONAL
12B2180X-RAY DIFFRACTIONPOSITIONAL0.03
21A1817X-RAY DIFFRACTIONPOSITIONAL
22B1817X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.9730.3791400.32526682808100
2.973-3.0530.3241390.29726432782100
3.053-3.1420.3231420.26626882830100
3.142-3.2440.2921400.24226642804100
3.244-3.360.241400.23626672807100
3.36-3.4940.2471420.2162684282699
3.494-3.6530.2361400.1962674281499
3.653-3.8450.2291410.1772664280599
3.845-4.0850.21420.162696283899
4.085-4.40.1881410.1342690283199
4.4-4.8410.1491420.1292681282398
4.841-5.5370.1651410.1382688282998
5.537-6.9620.1811440.1592727287197
6.962-29.9710.1961480.1582819296796
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)
11.123-0.552-0.00341.2863-0.46640.5989-0.0202-0.48610.0753-0.02790.0918-0.1485-0.04240.1639-00.4743-0.0265-0.06540.70580.04080.534552.510940.174313.3516
20.9171-0.36330.16310.93080.11611.367-0.1413-0.4082-0.40930.15070.00660.16210.1680.073-00.61690.020.10151.00120.29470.725225.026223.460533.6645
30.8611-0.0346-0.71051.1514-0.00271.2583-0.1385-0.482-0.52990.14240.04940.08620.36560.24580.00010.74820.1367-0.02260.91270.37020.824946.505310.150623.3901
4-0.0057-0-0.0092-0.0106-0.03260.0094-0.074-0.1289-0.0198-0.09710.1322-0.0161-0.076-0.0013-0.00021.3624-0.03280.10821.55740.24881.875137.249-3.52238.8343
51.0971-0.3917-0.20071.80090.05521.21490.0056-0.1338-0.3227-0.3754-0.03150.13630.3154-0.14710.00010.5896-0.0094-0.110.490.10010.6538.752117.467-5.2144
60.7339-0.25870.33750.8846-0.03171.13580.01230.1225-0.1078-0.46210.0112-0.3612-0.1020.348700.9008-0.04210.20920.75950.02330.716365.3435.034-26.0077
71.3558-0.1848-0.110.3587-0.40391.4319-0.0672-0.176-0.239-0.1583-0.019-0.43830.18240.43250.00010.61620.10280.04530.81060.11760.846270.588121.6467-2.8368
8-0.0115-0.0219-0.03510.06720.0033-0.0681-0.11410.09140.36980.2860.0340.1588-0.2708-0.03680.0021.09460.2237-0.16931.53150.4511.817777.537437.740810.5906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:180 )A2 - 180
2X-RAY DIFFRACTION2( CHAIN A AND RESID 181:353 )A181 - 353
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 354:465 OR RESID 478:572 ) )A354 - 465
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 354:465 OR RESID 478:572 ) )A478 - 572
5X-RAY DIFFRACTION4( CHAIN A AND RESID 466:476 )A466 - 476
6X-RAY DIFFRACTION5( CHAIN B AND RESID 2:180 )B2 - 180
7X-RAY DIFFRACTION6( CHAIN B AND RESID 181:353 )B181 - 353
8X-RAY DIFFRACTION7( CHAIN B AND ( RESID 354:465 OR RESID 478:572 ) )B354 - 465
9X-RAY DIFFRACTION7( CHAIN B AND ( RESID 354:465 OR RESID 478:572 ) )B478 - 572
10X-RAY DIFFRACTION8( CHAIN B AND RESID 466:476 )B466 - 476

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