4HXY | pdb_00004hxy

PlmKR1-Ketoreductase from the first module of phoslactomycin biosynthesis in Streptomyces sp. HK803

• PDB DOI: https://doi.org/10.2210/pdb4HXY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces sp. HK803
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-12 Released: 2013-07-10 
• Deposition Author(s): Whicher, J.R., Smith, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.188 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Structural and Stereochemical Analysis of a Modular Polyketide Synthase Ketoreductase Domain Required for the Generation of a cis-Alkene.

Bonnett, S.A., Whicher, J.R., Papireddy, K., Florova, G., Smith, J.L., Reynolds, K.A.

(2013) Chem Biol 20: 772-783

• PubMed: 23790488 
• DOI: https://doi.org/10.1016/j.chembiol.2013.04.014
• Primary Citation Related Structures: 
  4HXY


• PubMed Abstract: 
  

  The formation of an activated cis-3-cyclohexylpropenoic acid by Plm1, the first extension module of the phoslactomycin polyketide synthase, is proposed to occur through an L-3-hydroxyacyl-intermediate as a result of ketoreduction by an A-type ketoreductase (KR). Here, we demonstrate that the KR domain of Plm1 (PlmKR1) catalyzes the formation of an L-3-hydroxyacyl product. The crystal structure of PlmKR1 revealed a well-ordered active site with a nearby Trp residue characteristic of A-type KRs. Structural comparison of PlmKR1 with B-type KRs that produce D-3-hydroxyacyl intermediates revealed significant differences. The active site of cofactor-bound A-type KRs is in a catalysis-ready state, whereas cofactor-bound B-type KRs are in a precatalytic state. Furthermore, the closed lid loop in substrate-bound A-type KRs restricts active site access from all but one direction, which is proposed to control the stereochemistry of ketoreduction.

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Organizational Affiliation: 
• Department of Chemistry, Portland State University, Portland, OR. 97201.
Chemical Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109.
Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109.
Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.7 kDa 
• Atom Count: 7,408 
• Modeled Residue Count: 855 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plm1	A, B	438	Streptomyces sp. HK803	Mutation(s): 0  Gene Names: plm1
UniProt
Find proteins for Q6V1M8 (Streptomyces sp. HK803) Explore Q6V1M8  Go to UniProtKB:  Q6V1M8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
ACA	E [auth B]	6-AMINOHEXANOIC ACID C6 H13 N O2 SLXKOJJOQWFEFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.188 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.157	α = 90
b = 123.398	β = 90.27
c = 79.884	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Whicher, J.R., Smith, J.L.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations