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Entry
Database: PDB / ID: 4lrt
TitleCrystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site
Components
  • 4-hydroxy-2-oxovalerate aldolase
  • Acetaldehyde dehydrogenase
KeywordsLyase/OXIDOREDUCTASE / Rosmmann Fold / TIM barrel / Dehydrogenase / aldolase / Lyase-OXIDOREDUCTASE complex
Function / homology
Function and homology information


4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase activity / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / : / NAD binding / manganese ion binding
Similarity search - Function
DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain ...DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Helicase, Ruva Protein; domain 3 - #60 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / Helicase, Ruva Protein; domain 3 / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / PYRUVIC ACID / Acetaldehyde dehydrogenase / 4-hydroxy-2-oxovalerate aldolase
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFischer, B. / Branlant, G. / Talfournier, F. / Gruez, A.
CitationJournal: To be Published
Title: Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA ...Title: Crystal and solution structures of the bifunctional enzyme (Aldolase/Aldehyde dehydrogenase) from Thermomonospora curvata, reveal a cofactor-binding domain motion during NAD+ and CoA accommodation whithin the shared cofactor-binding site
Authors: Fischer, B. / Branlant, G. / Talfournier, F. / Gruez, A.
History
DepositionJul 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn_type.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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-2-oxovalerate aldolase
B: Acetaldehyde dehydrogenase
C: 4-hydroxy-2-oxovalerate aldolase
D: Acetaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,23019
Polymers142,9094
Non-polymers2,32015
Water24,5721364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-131 kcal/mol
Surface area41360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.500, 116.700, 131.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein 4-hydroxy-2-oxovalerate aldolase / / HOA / 4-hydroxy-2-keto-pentanoic acid aldolase / 4-hydroxy-2-oxopentanoate aldolase


Mass: 37326.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: DSM 43183 / Gene: Tcur_0536 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3)
References: UniProt: D1A3K8, 4-hydroxy-2-oxovalerate aldolase
#2: Protein Acetaldehyde dehydrogenase / / Acetaldehyde dehydrogenase [acetylating]


Mass: 34127.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: DSM 43183 / Gene: Tcur_0535 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3)
References: UniProt: D1A3K7, acetaldehyde dehydrogenase (acetylating)

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Non-polymers , 7 types, 1379 molecules

#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / References: 4-hydroxy-2-oxovalerate aldolase
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / References: acetaldehyde dehydrogenase (acetylating)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1364 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 26-34% PEG 4000 or 3350, 0.1 M Tris, 0.2 M Li2SO4, 0.005 M CoA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.5→46.45 Å / Num. all: 208563 / Num. obs: 812171 / % possible obs: 90 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.89 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 22.53
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.04 / % possible all: 52.5

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LRS

4lrs


Resolution: 1.5→46.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.166 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17016 10429 5 %RANDOM
Rwork0.15139 ---
obs0.15234 198134 100 %-
all-208563 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--0.23 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9307 0 142 1364 10813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02111172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.96815417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57351554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91924.032496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.154151763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.321596
X-RAY DIFFRACTIONr_chiral_restr0.140.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218953
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5951.57212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.021211732
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75933960
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8824.53684
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 445 -
Rwork0.206 8438 -
obs--100 %
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)
10.68360.06020.07720.21980.03450.26560.0104-0.0158-0.0962-0.0202-0.01930.00280.0261-0.00790.00890.00870.00380.00060.005-0.00160.030129.92-8.8034-21.2039
20.77970.31830.10890.5564-0.04620.44130.0054-0.1607-0.00550.0695-0.0309-0.0415-0.0427-0.00210.02550.02970.0103-0.0110.0416-0.00240.005254.98045.3479-1.3574
30.58450.12670.04860.3470.01490.18870.0129-0.05610.02930.0307-0.0041-0.0355-0.01160.0011-0.00880.016-0.00090.00430.0065-0.00720.0233-4.0783-9.6061-22.1537
40.5748-0.12420.1580.52180.09150.52020.02710.0324-0.0627-0.0381-0.02720.05420.0179-0.06180.00010.0212-0.0064-0.00070.0154-0.00660.0152-28.7846-26.9539-38.8626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 343
2X-RAY DIFFRACTION2B20 - 314
3X-RAY DIFFRACTION3C11 - 345
4X-RAY DIFFRACTION4D21 - 313

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