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- PDB-3oe1: Pyruvate decarboxylase variant Glu473Asp from Z. mobilis in compl... -

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Basic information

Entry
Database: PDB / ID: 3oe1
TitlePyruvate decarboxylase variant Glu473Asp from Z. mobilis in complex with reaction intermediate 2-lactyl-ThDP
ComponentsPyruvate decarboxylase
KeywordsLYASE
Function / homology
Function and homology information


pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
: / : / Thiamine pyrophosphate (TPP)-dependent enzyme / 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 (TPP)-dependent enzyme / 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
Chem-TDL / Pyruvate decarboxylase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.985 Å
AuthorsMeyer, D. / Neumann, P. / Parthier, C. / Tittmann, K.
CitationJournal: Biochemistry / Year: 2010
Title: Double duty for a conserved glutamate in pyruvate decarboxylase: evidence of the participation in stereoelectronically controlled decarboxylation and in protonation of the nascent carbanion/enamine intermediate .
Authors: Meyer, D. / Neumann, P. / Parthier, C. / Friedemann, R. / Nemeria, N. / Jordan, F. / Tittmann, K.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: 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: Pyruvate decarboxylase
B: Pyruvate decarboxylase
C: Pyruvate decarboxylase
D: Pyruvate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,24014
Polymers243,9054
Non-polymers2,33510
Water22,6271256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29030 Å2
ΔGint-193 kcal/mol
Surface area62370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.493, 165.356, 95.869
Angle α, β, γ (deg.)90.000, 108.930, 90.000
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is represented by the tetramer in the asymetric unit

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Components

#1: Protein
Pyruvate decarboxylase / PDC


Mass: 60976.297 Da / Num. of mol.: 4 / Mutation: E473D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: pdc, ZMO1360 / Production host: Escherichia coli (E. coli) / References: UniProt: P06672, pyruvate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TDL / 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM / 2-LACTYLTHIAMIN DIPHOSPHATE


Mass: 513.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N4O10P2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1256 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10-12% PEG 1500 ,50 mM MES, 5 mM citrate, 0.5 mM thiamine diphosphate, 3 mM magnesium sulfate, 2.5 mg/mL protein , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 22, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 128527 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 30.921 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.051 / Net I/σ(I): 16.57
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.98-2.10.1795.8458861852983.3
2.1-2.250.138.9618442110097.9
2.25-2.420.09811.8551361788997.1
2.42-2.650.07914.4544261730396.5
2.65-2.960.06118492591553595.6
2.96-3.40.04523.5421041326494.4
3.4-4.140.03628.8360011125492.5
4.14-5.720.03432.128026860091.1
5.72-100.03135.114156422389.8
10-200.02539.6275883085.5
20-30
30

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZPD

1zpd


Resolution: 1.985→19.584 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 6426 5 %RANDOM
Rwork0.1942 ---
all0.1968 128524 --
obs0.1968 128524 94.11 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.424 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso max: 137.8 Å2 / Biso mean: 26.392 Å2 / Biso min: 6.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.985→19.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16955 0 144 1256 18355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417488
X-RAY DIFFRACTIONf_angle_d0.92423804
X-RAY DIFFRACTIONf_chiral_restr0.0562651
X-RAY DIFFRACTIONf_plane_restr0.0033096
X-RAY DIFFRACTIONf_dihedral_angle_d13.76259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9851-2.00760.35241200.26892262238253
2.0076-2.03120.29932130.24894031424493
2.0312-2.05590.3142230.23714238446199
2.0559-2.08190.31442220.23424235445798
2.0819-2.10930.29362250.22264270449598
2.1093-2.13820.30372200.22134170439098
2.1382-2.16870.29582260.21534296452298
2.1687-2.2010.24732190.20334173439298
2.201-2.23530.24882240.20234244446898
2.2353-2.27190.29252180.20464173439197
2.2719-2.3110.24162210.19354200442197
2.311-2.3530.26382210.1914184440597
2.353-2.39820.26232230.20374242446597
2.3982-2.4470.2922190.20834165438497
2.447-2.50010.27182210.20454203442497
2.5001-2.55820.26392190.1944156437597
2.5582-2.6220.26032180.19164140435896
2.622-2.69270.24882200.18964188440897
2.6927-2.77180.27142170.19994120433796
2.7718-2.8610.24852170.20044126434396
2.861-2.96290.26662170.20154119433695
2.9629-3.08110.22912170.1864118433595
3.0811-3.22070.2452150.17944085430095
3.2207-3.38970.23662140.18064067428194
3.3897-3.60090.21362130.17194038425193
3.6009-3.87690.18682100.17114002421292
3.8769-4.26340.20892110.16524010422192
4.2634-4.8720.19512090.16913964417391
4.872-6.10720.23672090.19343967417691
6.1072-19.58530.22252050.20693912411789
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)
10.0164-0.0082-0.02460.72330.16620.6224-0.0255-0.02730.0724-0.03020.0282-0.0268-0.08070.13510.00660.0281-0.005-0.0240.0764-0.00230.120214.203816.283710.8872
20.20470.06580.1340.47220.12330.2174-0.0169-0.06660.1199-0.2266-0.05490.4125-0.1269-0.09150.06780.10210.0498-0.16470.0185-0.01750.3763-18.209630.73121.6715
30.07950.04820.11490.19640.01380.39630.0489-0.0497-0.15530.0183-0.10270.3979-0.099-0.19880.05510.10910.07780.00650.2346-0.16760.4517-25.704636.615830.3089
40.5541-0.3839-0.05110.63760.11160.1802-0.0577-0.04840.04720.1869-0.02260.197-0.0063-0.09110.0750.06240.02460.01720.0469-0.02690.1643-8.27324.412129.7469
50.20830.2601-0.10070.46010.15250.5859-0.03550.0043-0.06310.0989-0.02770.19690.1269-0.08070.07820.0735-0.00630.04890.0649-0.01090.1877-6.9301-4.012920.879
60.6415-0.37110.15520.47580.06080.4934-0.0389-0.1026-0.10660.1976-0.032-0.0930.41650.0676-0.02040.2030.1617-0.03830.0760.0260.10225.5051-20.09627.0129
70.4972-0.03210.43590.1141-0.13140.47670.0139-0.2753-0.05720.31850.182-0.16670.1828-0.1179-0.1550.22160.0041-0.18680.14580.01450.17333.58253.901750.2642
80.6412-0.18910.30450.47530.07980.2109-0.0819-0.1661-0.0150.23650.0798-0.09950.06710.0893-0.01030.1430.0625-0.03130.1322-0.01010.071215.45046.010238.7474
90.05280.03540.11380.69460.39880.4845-0.04290.0644-0.05060.07190.0451-0.01590.06620.0751-0.00580.04580.00740.00170.0719-0.01070.13513.83-16.356-3.3409
100.22410.10520.060.81170.6080.472-0.07620.0537-0.06860.3897-0.21620.43140.3402-0.18050.28560.2572-0.15220.25230.0948-0.13150.5258-19.0717-29.90745.3126
110.3354-0.0846-0.41820.7997-0.05581.0688-0.01420.2054-0.11260.03890.03280.38840.0727-0.0111-0.00910.1394-0.054-0.08790.1137-0.16340.543-26.6399-35.3403-23.1037
120.2785-0.05740.02180.72360.39580.38-0.07140.1752-0.1695-0.0841-0.11730.3830.0891-0.14160.17830.0566-0.0565-0.02050.0991-0.11360.3021-8.5631-23.8833-22.4489
130.165-0.10070.08720.33720.34520.7477-0.02430.03950.0054-0.1123-0.09860.2273-0.1381-0.06090.13650.05360.0017-0.07910.0611-0.02750.1847-6.564.4956-13.6551
140.59880.444-0.15540.45750.11510.5573-0.03980.1960.08-0.22960.0924-0.1872-0.31190.1781-0.06020.2138-0.09490.02140.17030.01190.155726.357319.6833-19.4525
150.68990.89160.26981.19660.36920.1127-0.02380.16770.0113-0.1633-0.02930.0072-0.1686-0.05220.06220.5013-0.0007-0.14070.4887-0.09250.363131.7846-5.4789-44.411
160.3968-0.0259-0.23920.52470.19860.4207-0.03610.186-0.0172-0.20570.0315-0.0845-0.09340.0763-0.00840.095-0.0497-0.00760.1155-0.01750.038415.6821-6.211-31.278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1:185)A1 - 185
2X-RAY DIFFRACTION2chain A and (resid 186:348)A186 - 348
3X-RAY DIFFRACTION3chain A and (resid 349:362)A349 - 362
4X-RAY DIFFRACTION4chain A and (resid 363:600)A363 - 600
5X-RAY DIFFRACTION5chain B and (resid 1:185)B1 - 185
6X-RAY DIFFRACTION6chain B and (resid 186:348)B186 - 348
7X-RAY DIFFRACTION7chain B and (resid 349:362)B349 - 362
8X-RAY DIFFRACTION8chain B and (resid 363:600)B363 - 600
9X-RAY DIFFRACTION9chain C and (resid 1:185)C1 - 185
10X-RAY DIFFRACTION10chain C and (resid 186:348)C186 - 348
11X-RAY DIFFRACTION11chain C and (resid 349:362)C349 - 362
12X-RAY DIFFRACTION12chain C and (resid 363:600)C363 - 600
13X-RAY DIFFRACTION13chain D and (resid 1:185)D1 - 185
14X-RAY DIFFRACTION14chain D and (resid 186:348)D186 - 348
15X-RAY DIFFRACTION15chain D and (resid 349:362)D349 - 362
16X-RAY DIFFRACTION16chain D and (resid 363:600)D363 - 600

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