7M7I

6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with antibody fragment 1B2 (TE-free)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mapping the catalytic conformations of an assembly-line polyketide synthase module.

Cogan, D.P.Zhang, K.Li, X.Li, S.Pintilie, G.D.Roh, S.H.Craik, C.S.Chiu, W.Khosla, C.

(2021) Science 374: 729-734

  • DOI: https://doi.org/10.1126/science.abi8358
  • Primary Citation of Related Structures:  
    7M7E, 7M7F, 7M7G, 7M7H, 7M7I, 7M7J

  • PubMed Abstract: 

    Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.


  • Organizational Affiliation

    Department of Chemistry, Stanford University, Stanford, CA 94305, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EryAIA [auth B],
B [auth A]
1,593Saccharopolyspora erythraeaMutation(s): 0 
Gene Names: eryAI
EC: 2.3.1.94
UniProt
Find proteins for Q5UNP6 (Saccharopolyspora erythraea)
Explore Q5UNP6 
Go to UniProtKB:  Q5UNP6
Find proteins for Q03131 (Saccharopolyspora erythraea)
Explore Q03131 
Go to UniProtKB:  Q03131
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ5UNP6Q03131
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1B2 (light chain)
C, E
249Saccharopolyspora erythraeaMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
1B2 (heavy chain)
D, F
236Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PN7
Query on PN7

Download Ideal Coordinates CCD File 
G [auth B]N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-SECBINFHSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary