5KP8

Crystal Structure of the Curacin Biosynthetic Pathway HMG Synthase in Complex with Acetyl Donor-ACP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Anatomy of the beta-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate.

Maloney, F.P.Gerwick, L.Gerwick, W.H.Sherman, D.H.Smith, J.L.

(2016) Proc Natl Acad Sci U S A 113: 10316-10321

  • DOI: https://doi.org/10.1073/pnas.1607210113
  • Primary Citation of Related Structures:  
    5KP5, 5KP6, 5KP7, 5KP8

  • PubMed Abstract: 

    Alkyl branching at the β position of a polyketide intermediate is an important variation on canonical polyketide natural product biosynthesis. The branching enzyme, 3-hydroxy-3-methylglutaryl synthase (HMGS), catalyzes the aldol addition of an acyl donor to a β-keto-polyketide intermediate acceptor. HMGS is highly selective for two specialized acyl carrier proteins (ACPs) that deliver the donor and acceptor substrates. The HMGS from the curacin A biosynthetic pathway (CurD) was examined to establish the basis for ACP selectivity. The donor ACP (CurB) had high affinity for the enzyme (Kd = 0.5 μM) and could not be substituted by the acceptor ACP. High-resolution crystal structures of HMGS alone and in complex with its donor ACP reveal a tight interaction that depends on exquisite surface shape and charge complementarity between the proteins. Selectivity is explained by HMGS binding to an unusual surface cleft on the donor ACP, in a manner that would exclude the acceptor ACP. Within the active site, HMGS discriminates between pre- and postreaction states of the donor ACP. The free phosphopantetheine (Ppant) cofactor of ACP occupies a conserved pocket that excludes the acetyl-Ppant substrate. In comparison with HMG-CoA (CoA) synthase, the homologous enzyme from primary metabolism, HMGS has several differences at the active site entrance, including a flexible-loop insertion, which may account for the specificity of one enzyme for substrates delivered by ACP and the other by CoA.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CurD443Moorena producens 3LMutation(s): 4 
Gene Names: LYNGBM3L_74540
EC: 2.3.3.10
UniProt
Find proteins for F4Y432 (Moorena producens 3L)
Explore F4Y432 
Go to UniProtKB:  F4Y432
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4Y432
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CurB102Lyngbya majusculaMutation(s): 0 
Gene Names: curB
UniProt
Find proteins for Q6DNF1 (Lyngbya majuscula)
Explore Q6DNF1 
Go to UniProtKB:  Q6DNF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DNF1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6VG
Query on 6VG

Download Ideal Coordinates CCD File 
D [auth B]~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate
C13 H25 N2 O8 P S
AJFWMDFTVVFMHY-NSHDSACASA-N
PNS
Query on PNS

Download Ideal Coordinates CCD File 
C [auth B]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.892α = 90
b = 100.892β = 90
c = 104.461γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01-DK042303
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA108874

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-14
    Changes: Database references
  • Version 1.2: 2016-09-21
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description