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- PDB-2vsu: A ternary complex of Hydroxycinnamoyl-CoA Hydratase-Lyase (HCHL) ... -

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Basic information

Entry
Database: PDB / ID: 2vsu
TitleA ternary complex of Hydroxycinnamoyl-CoA Hydratase-Lyase (HCHL) with acetyl-Coenzyme A and vanillin gives insights into substrate specificity and mechanism.
Components(P-HYDROXYCINNAMOYL COA ...) x 4
KeywordsLYASE / ALDOLASE / CROTONASE / HYDRATASE
Function / homology
Function and homology information


feruloyl-CoA hydratase/lyase / feruloyl-CoA hydratase/lyase activity / : / isoprenoid catabolic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / 4-hydroxy-3-methoxybenzaldehyde / Hydroxycinnamoyl-CoA hydratase-lyase
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBennett, J.P. / Bertin, L.M. / Brzozowski, A.M. / Walton, N.J. / Grogan, G.
CitationJournal: Biochem.J. / Year: 2008
Title: A Ternary Complex of Hydroxycinnamoyl-Coa Hydratase-Lyase (Hchl) with Acetyl-Coa and Vanillin Gives Insights Into Substrate Specificity and Mechanism.
Authors: Bennett, J.P. / Bertin, L. / Moulton, B. / Fairlamb, I.J.S. / Brzozowski, A.M. / Walton, N.J. / Grogan, G.
History
DepositionApr 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3May 4, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / database_PDB_caveat / pdbx_database_status / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 13, 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: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
B: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
C: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
D: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
E: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
F: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,24812
Polymers186,0486
Non-polymers4,2006
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29150 Å2
ΔGint-129.9 kcal/mol
Surface area48640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.081, 130.122, 144.743
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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P-HYDROXYCINNAMOYL COA ... , 4 types, 6 molecules ABDCEF

#1: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE S123A MUTANT


Mass: 31028.613 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH UK / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#2: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE S123A MUTANT


Mass: 30899.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-250,252-276 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH UK / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#3: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE S123A MUTANT


Mass: 31005.578 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH UK / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#4: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COA HYDRATASE-LYASE S123A MUTANT


Mass: 31056.629 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSTITUTE OF FOOD RESEARCH, NORWICH UK / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase

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Non-polymers , 3 types, 494 molecules

#5: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#6: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 123 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 123 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 123 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 123 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 123 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 123 TO ALA ENGINEERED RESIDUE IN CHAIN E, SER 123 TO ALA ENGINEERED RESIDUE IN CHAIN F, SER 123 TO ALA

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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: 2.3 Å3/Da / Density % sol: 46.1 % / Description: NONE
Crystal growDetails: PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO) ...Details: PROTEIN CONCENTRATION OF 10 MG ML-1 IN 11% (W/V) PEG 20 000 DA WITH 8% (V/V) PEG 550 DA MONOMETHYL ETHER, 0.8 M SODIUM FORMATE AND 0.2% (V/V) BUTANE 1,4-DIOL IN 0.05 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID BUFFER PH 5.6. 10MM FERULOYL-COA.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.9→96.67 Å / Num. obs: 123802 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5I

2j5i


Resolution: 1.9→96.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.755 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 6562 5 %RANDOM
Rwork0.188 ---
obs0.191 123802 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1.26 Å20 Å2
3---2.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→96.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11496 0 266 488 12250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.99116392
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07951485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87924.103524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.977152054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3361588
X-RAY DIFFRACTIONr_chiral_restr0.1090.21813
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029054
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.26312
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.28285
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2754
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3530.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9431.57597
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.338211748
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42735259
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5194.54642
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 390
Rwork0.283 7182
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)
10.79070.21350.18290.54480.11270.5845-0.10140.2474-0.1059-0.19650.1147-0.0164-0.00710.1723-0.01330.0016-0.06090.02960.0743-0.0279-0.098826.5118-32.4695-53.1548
20.40810.05580.25050.54030.21090.493-0.04810.00910.036-0.039-0.00940.20640.01730.00240.0575-0.0344-0.0226-0.0349-0.06220.01520.0415-3.6352-28.9431-37.4643
30.4645-0.11170.14410.90980.34580.4408-0.13620.10550.1801-0.28850.0740.0891-0.15850.08830.06220.0849-0.0923-0.122-0.04430.088-0.005212.1047-2.3034-51.1477
40.34520.15980.08250.4046-0.05290.33960.0052-0.06050.02340.0742-0.02430.06670.0064-0.02790.0191-0.0063-0.0020.0156-0.0152-0.0013-0.043311.1442-24.5809-10.5872
50.68610.150.2010.4580.09420.3486-0.01910.0799-0.04230.00340.0329-0.09070.0190.0738-0.0138-0.04580.0131-0.0219-0.00440.0055-0.019641.1936-26.8534-26.0133
60.47-0.00180.0660.51230.06060.2458-0.06560.02250.15330.05040.0161-0.0183-0.05890.04930.0496-0.0146-0.0214-0.0555-0.05680.01950.019825.5643.4973-23.6031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 249
2X-RAY DIFFRACTION2B4 - 250
3X-RAY DIFFRACTION3C5 - 249
4X-RAY DIFFRACTION4D3 - 248
5X-RAY DIFFRACTION5E4 - 249
6X-RAY DIFFRACTION6F3 - 248

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