1V07 | pdb_00001v07

CRYSTAL STRUCTURE OF ThrE11Val mutant of THE NERVE TISSUE MINI-HEMOGLOBIN FROM THE NEMERTEAN WORM CEREBRATULUS LACTEUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Thr-E11 Regulates O2 Affinity in Cerebratulus Lacteus Mini-Hemoglobin

Pesce, A.Nardini, M.Ascenzi, P.Geuens, E.Dewilde, S.Moens, L.Bolognesi, M.Riggs, A.Hale, A.Deng, P.Nienhaus, G.U.Olson, J.S.Nienhaus, K.

(2004) J Biological Chem 279: 33662

  • DOI: https://doi.org/10.1074/jbc.M403597200
  • Primary Citation of Related Structures:  
    1V07

  • PubMed Abstract: 

    The mini-hemoglobin from Cerebratulus lacteus (CerHb) belongs to a class of globins containing the polar Tyr-B10/Gln-E7 amino acid pair that normally causes low rates of O2 dissociation and ultra-high O2 affinity, which suggest O2 sensing or NO scavenging functions. CerHb, however, has high rates of O2 dissociation (kO2 = 200-600 s(-1)) and moderate O2 affinity (KO2) approximately 1 microm(-1)) as a result of a third polar amino acid in its active site, Thr-E11. When Thr-E11 is replaced by Val, kO2 decreases 1000-fold and KO2 increases 130-fold at pH 7.0, 20 degrees C. The mutation also shifts the stretching frequencies of both heme-bound and photodissociated CO, indicating marked changes of the electrostatic field at the active site. The crystal structure of Thr-E11 --> Val CerHbO2 at 1.70 A resolution is almost identical to that of the wild-type protein (root mean square deviation of 0.12 A). The dramatic functional and spectral effects of the Thr-E11 --> Val mutation are due exclusively to changes in the hydrogen bonding network in the active site. Replacing Thr-E11 with Val "frees" the Tyr-B10 hydroxyl group to rotate toward and donate a strong hydrogen bond to the heme-bound ligand, causing a selective increase in O2 affinity, a decrease of the rate coefficient for O2 dissociation, a 40 cm(-1) decrease in nuCO of heme-bound CO, and an increase in ligand migration toward more remote intermediate sites.


  • Organizational Affiliation

    Department of Physics-INFM and Center for Excellence in Biomedical Research, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEURAL HEMOGLOBIN110Cerebratulus lacteusMutation(s): 1 
UniProt
Find proteins for O76242 (Cerebratulus lacteus)
Explore O76242 
Go to UniProtKB:  O76242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76242
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.656α = 90
b = 43.422β = 90
c = 59.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other