2GNW

Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40W


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of phenylalanine B10 in plant nonsymbiotic hemoglobins.

Smagghe, B.J.Kundu, S.Hoy, J.A.Halder, P.Weiland, T.R.Savage, A.Venugopal, A.Goodman, M.Premer, S.Hargrove, M.S.

(2006) Biochemistry 45: 9735-9745

  • DOI: 10.1021/bi060716s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • All plants contain an unusual class of hemoglobins that display bis-histidyl coordination yet are able to bind exogenous ligands such as oxygen. Structurally homologous hexacoordinate hemoglobins (hxHbs) are also found in animals (neuroglobin and cyt ...

    All plants contain an unusual class of hemoglobins that display bis-histidyl coordination yet are able to bind exogenous ligands such as oxygen. Structurally homologous hexacoordinate hemoglobins (hxHbs) are also found in animals (neuroglobin and cytoglobin) and some cyanobacteria, where they are thought to play a role in free radical scavenging or ligand sensing. The plant hxHbs can be distinguished from the others because they are only weakly hexcacoordinate in the ferrous state, yet no structural mechanism for regulating hexacoordination has been articulated to account for this behavior. Plant hxHbs contain a conserved Phe at position B10 (Phe(B10)), which is near the reversibly coordinated distal His(E7). We have investigated the effects of Phe(B10) mutation on kinetic and equilibrium constants for hexacoordination and exogenous ligand binding in the ferrous and ferric oxidation states. Kinetic and equilibrium constants for hexacoordination and ligand binding along with CO-FTIR spectroscopy, midpoint reduction potentials, and the crystal structures of two key mutant proteins (F40W and F40L) reveal that Phe(B10) is an important regulatory element in hexacoordination. We show that Phe at this position is the only amino acid that facilitates stable oxygen binding to the ferrous Hb and the only one that promotes ligand binding in the ferric oxidation states. This work presents a structural mechanism for regulating reversible intramolecular coordination in plant hxHbs.


    Organizational Affiliation

    Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-symbiotic hemoglobin 1
A, B
165Oryza sativa subsp. japonicaMutation(s): 1 
Gene Names: HB1 (GLB1A)
Find proteins for O04986 (Oryza sativa subsp. japonica)
Go to UniProtKB:  O04986
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
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: 2.4 Å
  • R-Value Free: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.677α = 90.00
b = 125.677β = 90.00
c = 56.725γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
d*TREKdata scaling
CNSrefinement
d*TREKdata processing
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-04-11 
  • Released Date: 2006-04-25 
  • Deposition Author(s): Hoy, J.A.

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance