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- PDB-4lrs: Crystal and solution structures of the bifunctional enzyme (Aldol... -

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Basic information

Entry
Database: PDB / ID: 4lrs
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
  • Symmetric aldolase, C-terminal disordered residues
KeywordsOXIDOREDUCTASE / Rossmann fold / TIM barrel domain / Dehydrogenase / aldolase
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
FORMYL GROUP / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PYRUVIC ACID / Acetaldehyde dehydrogenase / 4-hydroxy-2-oxovalerate aldolase
Similarity search - Component
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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_ref_seq_dif / struct_sheet / 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_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.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_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_ref_seq_dif.details / _struct_sheet.number_strands / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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
N: Symmetric aldolase, C-terminal disordered residues
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,95423
Polymers71,6863
Non-polymers2,26820
Water10,178565
1
A: 4-hydroxy-2-oxovalerate aldolase
B: Acetaldehyde dehydrogenase
hetero molecules

A: 4-hydroxy-2-oxovalerate aldolase
B: Acetaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,44644
Polymers142,9094
Non-polymers4,53640
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area18570 Å2
ΔGint-129 kcal/mol
Surface area41360 Å2
MethodPISA
2
N: Symmetric aldolase, C-terminal disordered residues


  • defined by author&software
  • 231 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2311
Polymers2311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.880, 92.210, 56.480
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#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.: 1
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.: 1
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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Protein/peptide , 1 types, 1 molecules N

#3: Protein/peptide Symmetric aldolase, C-terminal disordered residues


Mass: 231.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: DSM 43183 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3)

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Non-polymers , 9 types, 585 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#11: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 26-34% PEG 4000 or 3350, 0.1 M Tris, 0.2 M Li2SO4, 0.005M NAD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
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
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: 1.55→43.35 Å / Num. obs: 424737 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.98 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.68
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.06 / % possible all: 85.2

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NVM

1nvm


Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.01 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.09 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2 5337 5 %RANDOM
Rwork0.164 ---
obs0.166 101394 97.7 %-
all-424737 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å21.03 Å2
2---1.1 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 145 565 5392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195350
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9747337
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65323.684228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44615811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7041546
X-RAY DIFFRACTIONr_chiral_restr0.0990.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214160
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.67335350
X-RAY DIFFRACTIONr_sphericity_free19.4955122
X-RAY DIFFRACTIONr_sphericity_bonded5.31655685
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 338 -
Rwork0.195 6419 -
obs--84.89 %
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)
10.9196-0.0521-0.00980.46370.01480.3128-0.00620.092-0.0314-0.03080.01980.05680.00330.0127-0.01360.1079-0.0039-0.00110.1160.0030.010156.766991.134917.2404
20.40250.2753-0.03371.37860.14270.4403-0.03810.07960.064-0.14540.02140.37830.0183-0.12250.01670.121-0.0131-0.04870.15750.02020.2215.649884.850212.6331
30.472-0.0591-0.08041.15880.0870.3420.0226-0.00820.1-0.00120.00530.1181-0.0507-0.0366-0.02790.09840.00130.00950.09430.00530.141731.8427101.085222.0027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 346
2X-RAY DIFFRACTION2B22 - 144
3X-RAY DIFFRACTION2B294 - 315
4X-RAY DIFFRACTION3B145 - 293

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