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- PDB-9msa: Alpha-ketoisovalerate decarboxylase (Kivd) from Synechocystis sp.... -

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Basic information

Entry
Database: PDB / ID: 9msa
TitleAlpha-ketoisovalerate decarboxylase (Kivd) from Synechocystis sp. PCC 6803 with substitution S286T
ComponentsAlpha-ketoisovalerate decarboxylase
KeywordsLYASE / Synechocystis / Isobutanol production / 3-Methyl-1-butanol / alpha-Ketoisovalerate decarboxylase / Kivd
Function / homology
Function and homology information


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 / : / 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-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Alpha-keto-acid decarboxylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsBegum, A. / Xie, H. / Gunn, L.H.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Energy AgencyP46607-1 Sweden
Vinnova2024-00443 Sweden
Swedish Research Council2019-06106 Sweden
CitationJournal: Biotechnol Biofuels Bioprod / Year: 2025
Title: Directed evolution of alpha-ketoisovalerate decarboxylase for improved isobutanol and 3-methyl-1-butanol production in cyanobacteria.
Authors: Xie, H. / Begum, A. / Gunn, L.H. / Lindblad, P.
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Alpha-ketoisovalerate decarboxylase
D: Alpha-ketoisovalerate decarboxylase
A: Alpha-ketoisovalerate decarboxylase
B: Alpha-ketoisovalerate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,14410
Polymers244,1214
Non-polymers1,0236
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-ketoisovalerate decarboxylase
D: Alpha-ketoisovalerate decarboxylase


Theoretical massNumber of molelcules
Total (without water)122,0602
Polymers122,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-25 kcal/mol
Surface area36600 Å2
MethodPISA
3
A: Alpha-ketoisovalerate decarboxylase
B: Alpha-ketoisovalerate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0848
Polymers122,0602
Non-polymers1,0236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-76 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.465, 81.731, 124.981
Angle α, β, γ (deg.)90.00, 105.52, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Alpha-ketoisovalerate decarboxylase


Mass: 61030.164 Da / Num. of mol.: 4 / Mutation: S286T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: kivd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q684J7
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 16 - 17.8 % (w/v) PEG6000 or PEG3350, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.79→40 Å / Num. obs: 53028 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.79→2.81 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.026 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4542 / CC1/2: 0.3 / % possible all: 99.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 48.581 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23391 2656 5 %RANDOM
Rwork0.18932 ---
obs0.19156 50371 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å20.89 Å2
2---1.67 Å20 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.79→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16304 0 62 29 16395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01216701
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.81622608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30152080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.644550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.889102944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.22572
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212512
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_it2.9764.8168347
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.768.65110418
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2834.8788354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.51549.3125106
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: 2.79→2.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 193 -
Rwork0.349 3674 -
obs--99.51 %
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)
12.0120.6149-0.69722.7081-1.26362.5994-0.07230.1960.4512-0.18010.1974-0.29020.09810.1233-0.12520.11780.0689-0.12290.39980.02510.452391.7479-45.25330.2174
21.10540.27-0.64452.4547-0.88273.07770.01230.08910.19550.23270.37520.92950.025-0.3048-0.38750.08390.1135-0.00940.43340.23830.746661.493-52.099522.867
32.82090.4448-0.04231.296-0.0421.03010.06340.24060.0588-0.17030.0073-0.3081-0.18940.104-0.07060.09670.04820.01740.2051-0.03060.185929.5674-35.609839.7192
42.72840.4935-0.11941.2059-0.03020.89850.02690.2063-0.1999-0.0552-0.01520.15890.035-0.1974-0.01170.02680.0392-0.05870.2306-0.06980.1586-5.0493-44.586445.81
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 528
2X-RAY DIFFRACTION2D1 - 528
3X-RAY DIFFRACTION3A1 - 602
4X-RAY DIFFRACTION4B1 - 602

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