1DTI

Recombinant sperm whale myoglobin h97d, d122n mutant (met)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Waterproofing the heme pocket. Role of proximal amino acid side chains in preventing hemin loss from myoglobin.

Liong, E.C.Dou, Y.Scott, E.E.Olson, J.S.Phillips Jr., G.N.

(2001) J.Biol.Chem. 276: 9093-9100

  • DOI: 10.1074/jbc.M008593200
  • Primary Citation of Related Structures:  1CH1, 1CH2, 1CH3, 1CH5, 1CH7, 1CH9, 1CIK, 1CIO, 1CO8, 1CO9, 1CP0, 1CP5, 1CPW

  • PubMed Abstract: 
  • The ability of myoglobin to bind oxygen reversibly depends critically on retention of the heme prosthetic group. Globin side chains at the Leu(89)(F4), His(97)(FG3), Ile(99)(FG5), and Leu(104)(G5) positions on the proximal side of the heme pocket str ...

    The ability of myoglobin to bind oxygen reversibly depends critically on retention of the heme prosthetic group. Globin side chains at the Leu(89)(F4), His(97)(FG3), Ile(99)(FG5), and Leu(104)(G5) positions on the proximal side of the heme pocket strongly influence heme affinity. The roles of these amino acids in preventing heme loss have been examined by determining high resolution structures of 14 different mutants at these positions using x-ray crystallography. Leu(89) and His(97) are important surface amino acids that interact either sterically or electrostatically with the edges of the porphyrin ring. Ile(99) and Leu(104) are located in the interior region of the proximal pocket beneath ring C of the heme prosthetic group. The apolar amino acids Leu(89), Ile(99), and Leu(104) "waterproof" the heme pocket by forming a barrier to solvent penetration, minimizing the size of the proximal cavity, and maintaining a hydrophobic environment. Substitutions with smaller or polar side chains at these positions result in exposure of the heme to solvent, the appearance of crystallographically defined water molecules in or near the proximal pocket, and large increases in the rate of hemin loss. Thus, the naturally occurring amino acid side chains at these positions serve to prevent hydration of the His(93)-Fe(III) bond and are highly conserved in all known myoglobins and hemoglobins.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (MYOGLOBIN)
A
154Physeter catodonGene 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: 1.7 Å
  • R-Value Free: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.163α = 90.00
b = 40.002β = 90.00
c = 80.011γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description