3M38

The roles of Glutamates and Metal ions in a rationally designed nitric oxide reductase based on myoglobin: I107E FeBMb (No metal ion binding to FeB site)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin.

Lin, Y.W.Yeung, N.Gao, Y.G.Miner, K.D.Tian, S.Robinson, H.Lu, Y.

(2010) Proc.Natl.Acad.Sci.USA 107: 8581-8586

  • DOI: 10.1073/pnas.1000526107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E ...

    A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative Fe(B) site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by approximately 110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu has a different role in redox tuning. More importantly, introducing the second Glu resulted in a approximately 100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the Fe(B) site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.


    Organizational Affiliation

    Department of Chemistry, George L. Clark X-Ray Facility and 3M Materials Laboratory, and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
153Physeter catodonMutation(s): 4 
Gene Names: MB
Find proteins for P02185 (Physeter catodon)
Go to Gene View: MB
Go to UniProtKB:  P02185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.850α = 90.00
b = 46.980β = 90.00
c = 77.670γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
SHELXphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance