4HBI

SCAPHARCA DIMERIC HEMOGLOBIN, MUTANT T72I, DEOXY FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mutational destabilization of the critical interface water cluster in Scapharca dimeric hemoglobin: structural basis for altered allosteric activity.

Pardanani, A.Gambacurta, A.Ascoli, F.Royer Jr., W.E.

(1998) J.Mol.Biol. 284: 729-739

  • DOI: 10.1006/jmbi.1998.2195
  • Primary Citation of Related Structures:  5HBI, 6HBI, 7HBI

  • PubMed Abstract: 
  • A cluster of interface ordered water molecules has been proposed to act as a key mediator of intersubunit communication in the homodimeric hemoglobin of Scapharca inaequivalvis. Mutations of Thr72 to Val and Ile, which lack the hydroxyl group to hydr ...

    A cluster of interface ordered water molecules has been proposed to act as a key mediator of intersubunit communication in the homodimeric hemoglobin of Scapharca inaequivalvis. Mutations of Thr72 to Val and Ile, which lack the hydroxyl group to hydrogen bond the deoxy interface water molecules, result in sharply altered functional properties. We have determined the high resolution (1.6-1. 8 A) crystal structures of these two mutants in both the deoxygenated and CO-liganded states. These structures show minimal protein structural changes relative to the same native derivatives, despite greater than 40-fold increases in oxygen affinity. In the deoxy state of both mutants two water molecules at the periphery of the water cluster are lost, and the remaining cluster water molecules are destabilized. The CO-liganded structures show key differences between the two mutants including a more optimal interface packing involving Ile72 that acts to stabilize its high affinity (R) state. This additional stabilization allows rationalization of its lowered cooperativity within the context of a two-state model. These studies support a key role of ordered water in cooperative functioning and illustrate how subtle structural alterations can result in significantly altered functional properties in an allosteric molecule.


    Related Citations: 
    • High-Resolution Crystallographic Analysis of a Co-Operative Dimeric Hemoglobin
      Royer Junior, W.E.
      (1994) J.Mol.Biol. 235: 657
    • A Single Mutation (Thr72-->Ile) at the Subunit Interface is Crucial for the Functional Properties of the Homodimeric Co-Operative Haemoglobin from Scapharca Inaequivalvis
      Gambacurta, A.,Piro, M.C.,Coletta, M.,Clementi, M.E.,Polizio, F.,Desideri, A.,Santucci, R.,Ascoli, F.
      (1995) J.Mol.Biol. 248: 910
    • Ordered Water Molecules as Key Allosteric Mediators in a Cooperative Dimeric Hemoglobin
      Royer Junior, W.E.,Pardanani, A.,Gibson, Q.H.,Peterson, E.S.,Friedman, J.M.
      (1996) Proc.Natl.Acad.Sci.USA 93: 14526


    Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester, MA, 01655, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN
A, B
146Anadara inaequivalvisN/A
Find proteins for P02213 (Anadara inaequivalvis)
Go to UniProtKB:  P02213
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: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 91.760α = 90.00
b = 44.320β = 90.00
c = 143.790γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
RIGAKUdata scaling
X-PLORmodel building
RIGAKUdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-06-24 
  • Released Date: 1998-11-11 
  • Deposition Author(s): Royer Junior, W.E.

Revision History 

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance