1EMY

CRYSTAL STRUCTURE OF ASIAN ELEPHANT (ELEPHAS MAXIMUS) CYANO-MET MYOGLOBIN AT 1.78 ANGSTROMS RESOLUTION. PHE 29 (B10) ACCOUNTS FOR ITS UNUSUAL LIGAND BINDING PROPERTIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of Asian elephant (Elephas maximus) cyano-metmyoglobin at 1.78-A resolution. Phe29(B10) accounts for its unusual ligand binding properties.

Bisig, D.A.Di Iorio, E.E.Diederichs, K.Winterhalter, K.H.Piontek, K.

(1995) J Biol Chem 270: 20754-20762

  • DOI: 10.1074/jbc.270.35.20754
  • Primary Citation of Related Structures:  
    1EMY

  • PubMed Abstract: 
  • The crystal structure of Asian elephant cyano-metmyoglobin which has a glutamine instead of the usual distal site histidine has been determined to high resolution. In addition to this replacement, the substitution of a conserved leucine residue in position 29(B10) at the distal side by a phenylalanine was unambiguously identified based on the available electron density ...

    The crystal structure of Asian elephant cyano-metmyoglobin which has a glutamine instead of the usual distal site histidine has been determined to high resolution. In addition to this replacement, the substitution of a conserved leucine residue in position 29(B10) at the distal side by a phenylalanine was unambiguously identified based on the available electron density. The suspicion, that there were errors in the original sequence which has caused some confusion, is thus confirmed. Comparison with other myoglobin structures in various ligated forms reveals an essentially unchanged tertiary structure in elephant myoglobin despite the two amino acid substitutions in the heme pocket. Our current structural model shows that the N epsilon 2 atom of Gln64(E7) has moved with respect to the corresponding nitrogen position of His64(E7) in the CO complex of sperm whale myoglobin. The newly assigned residue Phe29(B10) penetrates into the distal side of the heme pocket approaching the ligand within van der Waals distance and causing a much more crowded heme pocket compared to other myoglobins. Kinetic properties of Asian elephant myoglobin, wild type, and recombinant sperm whale myoglobins are discussed in relation to the structural consequences of the two amino acid substitutions H64Q and L29F.


    Related Citations: 
    • A Double Mutant of Sperm Whale Myoglobin Mimics the Structure and Function of Elephant Myoglobin
      Zhao, X., Vyas, K., Nguyen, B.D., Rajarathnam, K., La Mar, G.N., Li, T., Phillips Jr., G.N., Eich, R.F., Olson, J.S., Ling, J., Bocian, D.F.
      () To be published --: --
    • 1H NMR Investigation of the Heme Cavity of Elephant (E7 Gln) met-Cyano-Myoglobin. Evidence for a B-Helix Phenylalanine Interaction with Bound Ligand
      Vyas, K., Rajarathnam, K., Yu, L.P., Emerson, S.D., La Mar, G.N., Krishnamoorthi, R.
      (1993) J Biol Chem 268: 14826

    Organizational Affiliation

    Laboratory of Biochemistry I, Swiss Federal Institute of Technology, CH-8092 Zürich.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYOGLOBIN A153Elephas maximusMutation(s): 0 
Gene Names: MB
Find proteins for P02186 (Elephas maximus)
Explore P02186 
Go to UniProtKB:  P02186
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CYN
Query on CYN

Download Ideal Coordinates CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.51α = 90
b = 58.59β = 90
c = 70.44γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description