1GED | pdb_00001ged

A positive charge route for the access of nadh to heme formed in the distal heme pocket of cytochrome p450nor

• PDB DOI: https://doi.org/10.2210/pdb1GED/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Fusarium oxysporum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-11-02 Released: 2000-11-22 
• Deposition Author(s): Kudo, T., Takaya, N., Park, S.-Y., Shiro, Y., Shoun, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.279 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

A positively charged cluster formed in the heme-distal pocket of cytochrome P450nor is essential for interaction with NADH

Kudo, T., Takaya, N., Park, S.-Y., Shiro, Y., Shoun, H.

(2001) J Biological Chem 276: 5020-5026

• PubMed: 11076941 
• DOI: https://doi.org/10.1074/jbc.M007244200
• Primary Citation Related Structures: 
  1GED


• PubMed Abstract: 
  

  Arg and Lys residues are concentrated on the distal side of cytochrome P450nor (P450nor) to form a positively charged cluster facing from the outside to the inside of the distal heme pocket. We constructed mutant proteins in which the Arg and Lys residues were replaced with Glu, Gln, or Ala. The results showed that this cluster plays crucial roles in NADH interaction. We also showed that some anions such as bromide (Br(-)) perturbed the heme environment along with the reduction step in P450nor-catalyzed reactions, which was similar to the effects caused by the mutations. We determined by x-ray crystallography that a Br(-), termed an anion hole, occupies a key region neighboring heme, which is the terminus of the positively charged cluster and the terminus of the hydrogen bond network that acts as a proton delivery system. A comparison of the predicted mechanisms between the perturbations caused by Br(-) and the mutations suggested that Arg(174) and Arg(64) play a crucial role in binding NADH to the protein. These results indicated that the positively charged cluster is the unique structure of P450nor that responds to direct interaction with NADH.

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Organizational Affiliation: 
• Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.2 kDa 
• Atom Count: 3,250 
• Modeled Residue Count: 399 
• Deposited Residue Count: 403 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 55A1	A	403	Fusarium oxysporum	Mutation(s): 0  EC: 1.14 (PDB Primary Data), 1.7.1.14 (UniProt)
UniProt
Find proteins for P23295 (Fusarium oxysporum) Explore P23295  Go to UniProtKB:  P23295

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BR	B [auth A], C [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.279 (Depositor) 
• R-Value Work:  0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.32	α = 90
b = 78.05	β = 90
c = 86.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-22 
Deposition Author(s): Kudo, T., Takaya, N., Park, S.-Y., Shiro, Y., Shoun, H.

Revision History  

• Version 1.0: 2000-11-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description