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- PDB-1pzq: Structure of fused docking domains from the erythromycin polyketi... -

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Basic information

Entry
Database: PDB / ID: 1pzq
TitleStructure of fused docking domains from the erythromycin polyketide synthase (DEBS), a model for the interaction between DEBS 2 and DEBS 3: The A domain
ComponentsErythronolide synthase
KeywordsTRANSFERASE / FOUR HELIX BUNDLE / HOMODIMER
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Docking domain of the erythromycin polyketide synthase (DEBS) / Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : ...Docking domain of the erythromycin polyketide synthase (DEBS) / Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / 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, 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythronolide synthase EryA2
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBroadhurst, R.W. / Nietlispach, D. / Wheatcroft, M.P. / Leadlay, P.F. / Weissman, K.J.
CitationJournal: Chem.Biol. / Year: 2003
Title: The structure of docking domains in modular polyketide synthases.
Authors: Broadhurst, R.W. / Nietlispach, D. / Wheatcroft, M.P. / Leadlay, P.F. / Weissman, K.J.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erythronolide synthase
B: Erythronolide synthase


Theoretical massNumber of molelcules
Total (without water)12,8582
Polymers12,8582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Erythronolide synthase / ORF 2 / 6-deoxyerythronolide B synthase II / DEBS 2


Mass: 6428.874 Da / Num. of mol.: 2 / Fragment: C-terminal fragment / Mutation: L1G, F2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: ERYA / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS / Keywords: Insertion of GS at N-terminus
References: UniProt: Q03132, 6-deoxyerythronolide-B synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2213D 13C-separated NOESY
2323D 13C 15N X-filtered 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy. Intermolecular contacts were obtained from an X-filtered NOESY experiment on a mixed-labeled sample.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM DOCK23 U-15N,13C: 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O90% H2O/10% D2O
21mM DOCK23 (50% U-15N,13C: 50% unlabeled): 100mM phosphate buffer NA: trace amounts of sodium azide, AEBSF protease inhibitor cocktail and TSP 1H shift reference: 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate buffer NA / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
ANSIG3.3Kraulisdata analysis
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1811 restraints: 1709 NOE-derived distance constraints, 60 dihedral angle restraints, 42 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 8

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