4EIQ | pdb_00004eiq

Chromopyrrolic acid-soaked RebC-10x with bound 7-carboxy-K252c

• PDB DOI: https://doi.org/10.2210/pdb4EIQ/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Lentzea aerocolonigenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-04-05 Released: 2012-08-08 
• Deposition Author(s): Goldman, P.J., Ryan, K.S., Howard-Jones, A.R., Hamill, M.J., Elliott, S.J., Walsh, C.T., Drennan, C.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 

Literature

An Unusual Role for a Mobile Flavin in StaC-like Indolocarbazole Biosynthetic Enzymes.

Goldman, P.J., Ryan, K.S., Hamill, M.J., Howard-Jones, A.R., Walsh, C.T., Elliott, S.J., Drennan, C.L.

(2012) Chem Biol 19: 855-865

• PubMed: 22840773 
• DOI: https://doi.org/10.1016/j.chembiol.2012.05.016
• Primary Citation Related Structures: 
  4EIP, 4EIQ


• PubMed Abstract: 
  

  The indolocarbazole biosynthetic enzymes StaC, InkE, RebC, and AtmC mediate the degree of oxidation of chromopyrrolic acid on route to the natural products staurosporine, K252a, rebeccamycin, and AT2433-A1, respectively. Here, we show that StaC and InkE, which mediate a net 4-electron oxidation, bind FAD with a micromolar K(d), whereas RebC and AtmC, which mediate a net 8-electron oxidation, bind FAD with a nanomolar K(d) while displaying the same FAD redox properties. We further create RebC-10x, a RebC protein with ten StaC-like amino acid substitutions outside of previously characterized FAD-binding motifs and the complementary StaC-10x. We find that these mutations mediate both FAD affinity and product specificity, with RebC-10x displaying higher StaC activity than StaC itself. X-ray structures of this StaC catalyst identify the substrate of StaC as 7-carboxy-K252c and suggest a unique mechanism for this FAD-dependent enzyme.

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Organizational Affiliation: 
• Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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: 120.07 kDa 
• Atom Count: 7,928 
• Modeled Residue Count: 1,025 
• Deposited Residue Count: 1,098 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative FAD-monooxygenase	A, B	549	Lentzea aerocolonigenes	Mutation(s): 10  Gene Names: rbmD, rebC
UniProt
Find proteins for Q8KI25 (Lentzea aerocolonigenes) Explore Q8KI25  Go to UniProtKB:  Q8KI25

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KCT	C [auth A], D [auth B]	(5S)-7-oxo-6,7,12,13-tetrahydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5-carboxylic acid C21 H13 N3 O3 LYSTWLDKIFYXOG-IBGZPJMESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.255 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.184	α = 90
b = 77.703	β = 98.78
c = 123.145	γ = 90

Software Package:

Software Name	Purpose
APEX	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Goldman, P.J., Ryan, K.S., Howard-Jones, A.R., Hamill, M.J., Elliott, S.J., Walsh, C.T., Drennan, C.L.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations