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- PDB-8h6s: Structure of acyltransferase VinK in complex with the loading acy... -

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Basic information

Entry
Database: PDB / ID: 8h6s
TitleStructure of acyltransferase VinK in complex with the loading acyl carrier protein of vicenistatin PKS
Components
  • Malonyl-CoA-[acyl-carrier-protein] transacylase
  • Polyketide synthase modules 1-3
KeywordsTRANSFERASE / acyl carrier protein / polyketide synthase / acyltransferase
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / DIM/DIP cell wall layer assembly / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding ...[acyl-carrier-protein] S-malonyltransferase / DIM/DIP cell wall layer assembly / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / VinK acyltransferase small domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...: / VinK acyltransferase small domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-9EF / Polyketide synthase modules 1-3 / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKawada, K. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
Japan Society for the Promotion of Science (JSPS)17K07747 Japan
CitationJournal: Biochemistry / Year: 2023
Title: Structural Basis of Transient Interactions of Acyltransferase VinK with the Loading Acyl Carrier Protein of the Vicenistatin Modular Polyketide Synthase.
Authors: Miyanaga, A. / Kawada, K. / Chisuga, T. / Kudo, F. / Eguchi, T.
History
DepositionOct 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malonyl-CoA-[acyl-carrier-protein] transacylase
B: Malonyl-CoA-[acyl-carrier-protein] transacylase
C: Polyketide synthase modules 1-3
D: Polyketide synthase modules 1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5818
Polymers105,7664
Non-polymers8154
Water21612
1
A: Malonyl-CoA-[acyl-carrier-protein] transacylase
C: Polyketide synthase modules 1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2914
Polymers52,8832
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Malonyl-CoA-[acyl-carrier-protein] transacylase
D: Polyketide synthase modules 1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2914
Polymers52,8832
Non-polymers4082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.363, 90.626, 113.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A19 - 317
2010B19 - 317
1020C13 - 106
2020D13 - 106

NCS ensembles :
ID
1
2

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Components

#1: Protein Malonyl-CoA-[acyl-carrier-protein] transacylase


Mass: 38170.211 Da / Num. of mol.: 2 / Mutation: S106C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinK / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY5
#2: Protein Polyketide synthase modules 1-3


Mass: 14712.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinP1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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 % sol: 35.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, magnesium chloride, Tris-HCl, and D-glucose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16764 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.173 / Net I/σ(I): 9.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2385 / CC1/2: 0.735 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZD

5czd


Resolution: 3→46.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.672 / SU ML: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 814 4.9 %RANDOM
Rwork0.21 ---
obs0.2129 15908 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.81 Å2 / Biso mean: 64.029 Å2 / Biso min: 23.03 Å2
Baniso -1Baniso -2Baniso -3
1-6.81 Å20 Å20 Å2
2---5.91 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 3→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 50 12 6113
Biso mean--73.35 36.81 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175839
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6558463
X-RAY DIFFRACTIONr_angle_other_deg1.7481.5813419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.04220.171351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26515977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6991565
X-RAY DIFFRACTIONr_chiral_restr0.050.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021405
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90210.06
12B90210.06
21C28700.08
22D28700.08
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 40 -
Rwork0.342 1159 -
all-1199 -
obs--100 %

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