5KP7 | pdb_00005kp7

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

• PDB DOI: https://doi.org/10.2210/pdb5KP7/pdb

• Classification: TRANSFERASE
• Organism(s): Moorena producens 3L, Lyngbya majuscula
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-07-02 Released: 2016-08-31 
• Deposition Author(s): Maloney, F.P., Smith, J.L.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.167 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Models: experimental

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

• PubMed: 27573844 
• DOI: https://doi.org/10.1073/pnas.1607210113
• Primary Citation 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.

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Organizational Affiliation: 
• 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;
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 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; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.36 kDa 
• Atom Count: 4,220 
• Modeled Residue Count: 489 
• Deposited Residue Count: 546 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CurD	A	443	Moorena producens 3L	Mutation(s): 3  Gene Names: LYNGBM3L_74540 EC: 2.3.3.10
UniProt
Find proteins for F4Y432 (Moorena producens 3L) Explore F4Y432  Go to UniProtKB:  F4Y432

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CurB	B	103	Lyngbya majuscula	Mutation(s): 0  Gene Names: curB
UniProt
Find proteins for Q6DNF1 (Lyngbya majuscula) Explore Q6DNF1  Go to UniProtKB:  Q6DNF1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNS	E [auth B]	4'-PHOSPHOPANTETHEINE C11 H23 N2 O7 P S JDMUPRLRUUMCTL-VIFPVBQESA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.167 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.117	α = 90
b = 101.117	β = 90
c = 104.595	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Maloney, F.P., Smith, J.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01-DK042303
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01-CA108874

Revision History  

• 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