3NMM

Human Hemoglobin A mutant alpha H58W deoxy-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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This is version 1.1 of the entry. See complete history


Literature

Blocking the gate to ligand entry in human hemoglobin.

Birukou, I.Soman, J.Olson, J.S.

(2011) J Biol Chem 286: 10515-10529

  • DOI: 10.1074/jbc.M110.176271
  • Primary Citation of Related Structures:  
    3NL7, 3NML, 3NMM, 3OGB

  • PubMed Abstract: 
  • His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states ...

    His(E7) to Trp replacements in HbA lead to markedly biphasic bimolecular CO rebinding after laser photolysis. For isolated mutant subunits, the fraction of fast phase increases with increasing [CO], suggesting a competition between binding to an open conformation with an empty E7 channel and relaxation to blocked or closed, slowly reacting states. The rate of conformational relaxation of the open state is ∼18,000 s(-1) in α subunits and ∼10-fold faster in β subunits, ∼175,000 s(-1). Crystal structures were determined for tetrameric α(WT)β(Trp-63) HbCO, α(Trp-58)β(WT) deoxyHb, and Trp-64 deoxy- and CO-Mb as controls. In Trp-63(E7) βCO, the indole side chain is located in the solvent interface, blocking entry into the E7 channel. Similar blocked Trp-64(E7) conformations are observed in the mutant Mb crystal structures. In Trp-58(E7) deoxy-α subunits, the indole side chain fills both the channel and the distal pocket, forming a completely closed state. The bimolecular rate constant for CO binding, k'(CO), to the open conformations of both mutant Hb subunits is ∼80-90 μm(-1) s(-1), whereas k'(CO) for the completely closed states is 1000-fold slower, ∼0.08 μm(-1) s(-1). A transient intermediate with k'(CO) ≈ 0.7 μm(-1) s(-1) is observed after photolysis of Trp-63(E7) βCO subunits and indicates that the indole ring blocks the entrance to the E7 channel, as observed in the crystal structures of Trp(E7) deoxyMb and βCO subunits. Thus, either blocking or completely filling the E7 channel dramatically slows bimolecular binding, providing strong evidence that the E7 channel is the major pathway (≥90%) for ligand entry in human hemoglobin.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology and the W. M. Keck Center for Computational Biology, Rice University, Houston, Texas 77005, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit alphaA, C141Homo sapiensMutation(s): 1 
Gene Names: HBA1HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
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UniProt GroupP69905
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemoglobin subunit betaB, D146Homo sapiensMutation(s): 0 
Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
Entity Groups  
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UniProt GroupP68871
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.55α = 90
b = 81.83β = 99.76
c = 53.45γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance