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- PDB-7cpx: Lovastatin nonaketide synthase -

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Basic information

Entry
Database: PDB / ID: 7cpx
TitleLovastatin nonaketide synthase
ComponentsLovastatin nonaketide synthase, polyketide synthase component
KeywordsBIOSYNTHETIC PROTEIN / polyketide synthase
Function / homology
Function and homology information


malonyl-CoA metabolic process / lovastatin nonaketide synthase / lovastatin nonaketide synthase activity / lovastatin biosynthetic process / : / polyketide synthase activity / polyketide biosynthetic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups ...malonyl-CoA metabolic process / lovastatin nonaketide synthase / lovastatin nonaketide synthase activity / lovastatin biosynthetic process / : / polyketide synthase activity / polyketide biosynthetic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / methylation / oxidoreductase activity / ATP binding
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase N-terminal domain / Condensation domain / Condensation domain / Polyketide synthase, dehydratase domain / PKS_DH / : / 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. / Chloramphenicol acetyltransferase-like domain superfamily / Acyl transferase domain superfamily / Thiolase/Chalcone synthase / Acyl transferase/acyl hydrolase/lysophospholipase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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 / Thiolase-like / Vaccinia Virus protein VP39 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Lovastatin nonaketide synthase, polyketide synthase component
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsWang, J. / Wang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31470830 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the biosynthesis of lovastatin.
Authors: Jialiang Wang / Jingdan Liang / Lu Chen / Wei Zhang / Liangliang Kong / Chao Peng / Chen Su / Yi Tang / Zixin Deng / Zhijun Wang /
Abstract: Statins are effective cholesterol-lowering drugs. Lovastatin, one of the precursors of statins, is formed from dihydromonacolin L (DML), which is synthesized by lovastatin nonaketide synthase (LovB), ...Statins are effective cholesterol-lowering drugs. Lovastatin, one of the precursors of statins, is formed from dihydromonacolin L (DML), which is synthesized by lovastatin nonaketide synthase (LovB), with the assistance of a separate trans-acting enoyl reductase (LovC). A full DML synthesis comprises 8 polyketide synthetic cycles with about 35 steps. The assembling of the LovB-LovC complex, and the structural basis for the iterative and yet permutative functions of the megasynthase have remained a mystery. Here, we present the cryo-EM structures of the LovB-LovC complex at 3.60 Å and the core LovB at 2.91 Å resolution. The domain organization of LovB is an X-shaped face-to-face dimer containing eight connected domains. The binding of LovC laterally to the malonyl-acetyl transferase domain allows the completion of a L-shaped catalytic chamber consisting of six active domains. This architecture and the structural details of the megasynthase provide the basis for the processing of the intermediates by the individual catalytic domains. The detailed architectural model provides structural insights that may enable the re-engineering of the megasynthase for the generation of new statins.
History
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
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Revision 1.1Dec 15, 2021Group: Database references / Structure summary
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Assembly

Deposited unit
A: Lovastatin nonaketide synthase, polyketide synthase component
B: Lovastatin nonaketide synthase, polyketide synthase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)674,3804
Polymers672,8932
Non-polymers1,4872
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12320 Å2
ΔGint-43 kcal/mol
Surface area150830 Å2

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Components

#1: Protein Lovastatin nonaketide synthase, polyketide synthase component / LNKS / Lovastatin biosynthesis cluster protein B


Mass: 336446.656 Da / Num. of mol.: 2 / Mutation: G1884Q, Q1885A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: lovB / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q9Y8A5, lovastatin nonaketide synthase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Lovastatin nonaketide synthase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 335 kDa/nm / Experimental value: YES
Source (natural)Organism: Aspergillus terreus (mold)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was homogenous
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205047 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00170284
ELECTRON MICROSCOPYf_angle_d0.478126916
ELECTRON MICROSCOPYf_dihedral_angle_d9.94628394
ELECTRON MICROSCOPYf_chiral_restr0.0385478
ELECTRON MICROSCOPYf_plane_restr0.00210548

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