Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 144.99 kDa 
• Atom Count: 11093 
• Modelled Residue Count: 1213 
• Deposited Residue Count: 1242 
• Unique protein chains: 1

4YAW

Reduced CYPOR mutant - G141del

• PDB DOI: 10.2210/pdb4YAW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-17 Released: 2016-03-02 
• Deposition Author(s): Xia, C., Kim, J.J.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Literature

Mutants of Cytochrome P450 Reductase Lacking Either Gly-141 or Gly-143 Destabilize Its FMN Semiquinone.

Rwere, F., Xia, C., Im, S., Haque, M.M., Stuehr, D.J., Waskell, L., Kim, J.J.

(2016) J Biol Chem 291: 14639-14661

• PubMed: 27189945 
• DOI: 10.1074/jbc.M116.724625
• Primary Citation of Related Structures:  
  4Y7C, 4Y9R, 4Y9U, 4YAF, 4YAL, 4YAO, 4YAU, 4YAW


• PubMed Abstract: 
  

NADPH-cytochrome P450 oxidoreductase transfers electrons from NADPH to cytochromes P450 via its FAD and FMN. To understand the biochemical and structural basis of electron transfer from FMN-hydroquinone to its partners, three deletion mutants in a conserved loop near the FMN were characterized. Comparison of oxidized and reduced wild type and mutant structures reveals that the basis for the air stability of the neutral blue semiquinone is protonation of the flavin N5 and strong H-bond formation with the Gly-141 carbonyl. The ΔGly-143 protein had moderately decreased activity with cytochrome P450 and cytochrome c It formed a flexible loop, which transiently interacts with the flavin N5, resulting in the generation of both an unstable neutral blue semiquinone and hydroquinone. The ΔGly-141 and ΔG141/E142N mutants were inactive with cytochrome P450 but fully active in reducing cytochrome c In the ΔGly-141 mutants, the backbone amide of Glu/Asn-142 forms an H-bond to the N5 of the oxidized flavin, which leads to formation of an unstable red anionic semiquinone with a more negative potential than the hydroquinone. The semiquinone of ΔG141/E142N was slightly more stable than that of ΔGly-141, consistent with its crystallographically demonstrated more rigid loop. Nonetheless, both ΔGly-141 red semiquinones were less stable than those of the corresponding loop in cytochrome P450 BM3 and the neuronal NOS mutant (ΔGly-810). Our results indicate that the catalytic activity of cytochrome P450 oxidoreductase is a function of the length, sequence, and flexibility of the 140s loop and illustrate the sophisticated variety of biochemical mechanisms employed in fine-tuning its redox properties and function.

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Organizational Affiliation: 

the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH--cytochrome P450 reductase	A, B	621	Rattus norvegicus	Mutation(s): 0  Gene Names: Por EC: 1.6.2.4
UniProt
Find proteins for P00388 (Rattus norvegicus) Explore P00388  Go to UniProtKB:  P00388

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], J [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN	C [auth A], I [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
2AM	E [auth A], K [auth B]	ADENOSINE-2'-MONOPHOSPHATE C10 H14 N5 O7 P QDFHPFSBQFLLSW-KQYNXXCUSA-N
PO4	F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
2AM	BindingDB:  4YAW	-TΔS: 28.83 (kJ/mol) from 1 assay(s)
		ΔG: -2.93e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.462	α = 90
b = 116.035	β = 90
c = 118.487	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-02-17 
• Released Date: 2016-03-02 
Deposition Author(s): Xia, C., Kim, J.J.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM097031

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2016-07-20
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2018-03-07
  Changes: Data collection
• Version 1.5: 2019-12-25
  Changes: Author supporting evidence