5KP7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.USA 113: 10316-10321

  • DOI: 10.1073/pnas.1607210113
  • Primary Citation of Related Structures:  

  • 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 d ...

    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

    Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093;,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109;,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109;,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093;,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 JanetSmith@umich.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CurD
A
443Moorea producens 3LMutation(s): 3 
EC: 2.3.3.10
Find proteins for F4Y432 (Moorea producens 3L)
Go to UniProtKB:  F4Y432
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CurB
B
103Lyngbya majusculaMutation(s): 0 
Gene Names: curB
Find proteins for Q6DNF1 (Lyngbya majuscula)
Go to UniProtKB:  Q6DNF1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PNS
Query on PNS

Download SDF File 
Download CCD File 
B
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.151 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.117α = 90.00
b = 101.117β = 90.00
c = 104.595γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01-DK042303
National Institutes of Health/National Cancer InstituteUnited StatesR01-CA108874

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations