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- PDB-1kyz: Crystal Structure Analysis of Caffeic acid/5-hydroxyferulic acid ... -

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Basic information

Entry
Database: PDB / ID: 1kyz
TitleCrystal Structure Analysis of Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase Ferulic Acid Complex
ComponentsCaffeic acid 3-O-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase / lignin / ferulic acid / methylation
Function / homology
Function and homology information


caffeate O-methyltransferase / caffeate O-methyltransferase activity / phenylpropanoid biosynthetic process / lignin biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Caffeic acid 3-O-methyltransferase
Similarity search - Component
Biological speciesMedicago sativa (alfalfa)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZubieta, C. / Kota, P. / Ferrer, J.-L. / Dixon, R.A. / Noel, J.P.
CitationJournal: Plant Cell / Year: 2002
Title: Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase.
Authors: Zubieta, C. / Kota, P. / Ferrer, J.L. / Dixon, R.A. / Noel, J.P.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caffeic acid 3-O-methyltransferase
C: Caffeic acid 3-O-methyltransferase
E: Caffeic acid 3-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7069
Polymers119,9703
Non-polymers1,7366
Water4,756264
1
A: Caffeic acid 3-O-methyltransferase
E: Caffeic acid 3-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1376
Polymers79,9802
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-67 kcal/mol
Surface area28680 Å2
MethodPISA
2
C: Caffeic acid 3-O-methyltransferase
hetero molecules

C: Caffeic acid 3-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1376
Polymers79,9802
Non-polymers1,1574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)103.729, 61.865, 111.229
Angle α, β, γ (deg.)90.00, 112.18, 90.00
Int Tables number3
Space group name H-MP121
DetailsThe biological assembly is a dimer of

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Components

#1: Protein Caffeic acid 3-O-methyltransferase / COMT


Mass: 39990.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago sativa (alfalfa) / Production host: Escherichia coli (E. coli) / References: UniProt: P28002, caffeate O-methyltransferase
#2: Chemical ChemComp-FER / 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID / FERULIC ACID


Mass: 194.184 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H10O4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, calcium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMHEPES-Na1droppH7.5
2100 mM1dropNaCl
31 mMdithiothreitol1drop
425 mg/mlprotein1drop
512 %(w/v)PEG80001reservoir
60.05 MTAPS-Na+1reservoirpH8.5
70.25 Mcalcium acetate1reservoir
82. mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 12, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. all: 68292 / Num. obs: 66087 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.4 Å2
Reflection shellResolution: 2.19→2.23 Å / % possible all: 91
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 88232 / % possible obs: 98 % / Num. measured all: 388692 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.51

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partial seleno-methionine model (unpublished)

Resolution: 2.2→61.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1238884.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3295 5 %RANDOM
Rwork0.236 ---
all0.236 68292 --
obs0.236 65343 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1423 Å2 / ksol: 0.361389 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å28.09 Å2
2---0.87 Å20 Å2
3----1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→61.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8210 0 120 264 8594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it2.932
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 549 5 %
Rwork0.267 10356 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SAH_PARA.TXTSAH_TOPO.TXT
X-RAY DIFFRACTION3FER_PARA.TXTFER_TOPO.TXT
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 99 Å / % reflection Rfree: 5 % / Rfactor obs: 0.236 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.267

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