1GDJ

CRYSTAL STRUCTURE OF FERRIC COMPLEXES OF THE YELLOW LUPIN LEGHEMOGLOBIN WITH ISOQUINOLINE AT 1.8 ANGSTROMS RESOLUTION (RUSSIAN)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Structure of Deoxy- and Oxy-Leghaemoglobin from Lupin

Harutyunyan, H.E.Safonova, T.N.Kuranova, I.P.Popov, A.N.Teplyakov, A.V.Obmolova, G.V.Rusakov, A.A.Vainshtein, B.K.Dodson, G.G.Wilson, J.C.Perutz, M.F.

(1995) J.Mol.Biol. 251: 104-115

  • Primary Citation of Related Structures:  2GDM

  • PubMed Abstract: 
  • The leghaemoglobins have oxygen affinities 11 to 24 times higher than that of sperm whale myoglobin, due mainly to higher rates of association. To find out why, we have determined the structures of deoxy- and oxy-leghaemoglobin II of the lupin at 1.7 ...

    The leghaemoglobins have oxygen affinities 11 to 24 times higher than that of sperm whale myoglobin, due mainly to higher rates of association. To find out why, we have determined the structures of deoxy- and oxy-leghaemoglobin II of the lupin at 1.7 A resolution. Results confirm the general features found in previous X-ray analyses of this protein. The unique feature that has now emerged is the rotational freedom of the proximal histidine. In deoxy-leghaemoglobin the imidazole oscillates between two alternative orientations, eclipsing either the lines N1-N3 or N2-N4 of the porphyrin; in oxy-leghaemoglobin it is fixed in a staggered orientation. The iron atom moves from a position 0.30 A from the plane of the pyrrole nitrogen atoms in deoxy- to a position in the plane in oxy-leghaemoglobin while the Fe- bond distance remains constant at 2.02 A. The Fe-O-O angle is 152 degrees, as in human haemoglobin. The oxygen is hydrogen-bonded to the distal histidine at N epsilon 2-O1 and N epsilon 2-O2 distance of 2.95 A and 2.68 A, respectively. The porphyrin is ruffled equally in deoxy- and oxy-leghaemoglobins, due to rotations of the pyrrols about the N-Fe-N bonds, causing the methine bridges to deviate by up to 0.32 A from the mean porphyrin plane. The only feature capable of accounting for the high on-rate of the reaction with oxygen are the mobilities of the proximal histidine and distal histidine residues in deoxy-leghaemoglobin. The eclipsed positions of the proximal histidine in deoxy-leghaemoglobin maximize steric hindrance with the porphyrin nitrogen atoms and minimize pi-->p electron donation, while its staggered position in oxy-leghaemoglobin reverses both these effects. Together with the oscillation of the imidazole between the two orientations, these two factors may reduce the activation energy for the reaction of leghaemoglobin with oxygen. The distal histidine is in a fixed position in the haem pocket in the crystal, but must be swinging in and out of the pocket at a high rate in solution to allow the oxygen to enter.


    Related Citations: 
    • X-Ray Diffraction Study of Leghemoglobin. Iv. Determination of the Structure with 2.8 Angstroms Resolution (Russian)
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Nekrasov, Yu.V.
      (1978) Kristallografiya 23: 517
    • X-Ray Determination of Three-Dimensional Structure of Leghemoglobin from Lupinus Luteus L. At 5 Angstroms Resolution (Russian)
      Vainshtein, B.K.,Arutiunian, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1974) Dokl.Akad.Nauk Sssr 216: 690
    • Crystal Structure of Ferric Complexes of the Yellow Lupin Leghemoglobin with Isoquinoline at 1.8 Angstroms Resolution (Russian)
      Safonova, T.N.,Teplyakov, A.V.,Obmolova, G.V.,Popov, A.N.,Kuranova, I.P.,Harutyunyan, E.G.
      (1991) Bioorg.Khim. 17: 1605
    • The Haem-Accessibility in Leghaemoglobin of Lupinus Luteus as Observed by Proton Magnetic Relaxation
      Vuk-Pavlovic, S.,Benko, B.,Maricic, S.,Lahajnar, G.,Kuranova, I.P.,Vainshtein, B.K.
      (1976) Int.J.Pept.Protein Res. 8: 427
    • X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data on the Structure of the First Component (Russian)
      Arutyunyan, E.G.,Kuranova, I.P.,Grebenko, A.I.,Voronova, A.A.
      (1977) Kristallografiya 22: 634
    • Cell Parameters of Crystalline Plant (Lupinus Luteus (Lupine)) Hemoglobin (Russian)
      Arutyunyan, E.G.,Zaitsev, V.N.,Zhiznevskaya, G.Ya.,Borodenko, L.I.
      (1971) Kristallografiya 16: 237
    • Structure of Leghaemoglobin from Lupin Root Nodules at 5 Angstroms Resolution
      Vainshtein, B.K.,Harutyunyan, E.H.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovsky, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1975) Nature 254: 163
    • The X-Ray Structural Study of Leghemoglobin. II. Determination of the Structure at 5 Angstroms Resolution (Russian)
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1974) Kristallografiya 19: 971
    • X-Ray Study of Leghemoglobin. II. Determination of the Structure with Resolution of 5 Angstroms
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1975) Sov.Phys.Crystallogr.(Engl.Transl.) 19: 602
    • X-Ray Structural Study of Leghemoglobin. III. Crystallographic Data Regarding the Structure of the First Component
      Arutyunyan, E.G.,Kuranova, I.P.,Grebenko, A.I.,Voronova, A.A.
      (1977) Sov.Phys.Crystallogr.(Engl.Transl.) 22: 362
    • X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms
      Arutyunyan, E.G.,Kuranova, I.P.,Vainshtein, B.K.,Steigemann, W.
      (1980) Sov.Phys.Crystallogr.(Engl.Transl.) 25: 43
    • X-Ray Structure of Ferrous Complexes of the Yellow Lupin Leghemoglobin with Co and No at 1.8 Angstroms Resolution (Russian)
      Obmolova, G.V.,Safonova, T.N.,Teplyakov, A.V.,Popov, A.N.,Kuranova, I.P.,Harutyunyan, E.G.,Vainshtein, B.K.
      (1988) Bioorg.Khim. 14: 1509
    • Spatial Structure of Lupine Leghemoglobin with the 2.8 Angstroms Resolution (Russian)
      Vainshtein, B.K.,Arutiunian, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.,Nekrasov, Iu.V.
      (1977) Dokl.Akad.Nauk Sssr 233: 238
    • X-Ray Study of Leghemoglobin. I.Purification, Crystallization, and Preparation of Derivatives Containing Heavy Atoms
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1975) Sov.Phys.Crystallogr.(Engl.Transl.) 19: 598
    • Three-Dimensional Structure of Lupine Leghemoglobin with a Resolution of 2.8 Angstroms
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.,Nekrasov, Yu.V.
      (1977) Dokl.Biochem.(Engl.Transl.) 233: 67
    • X-Ray Diffraction Determination of the Three-Dimensional Structure of Leghemoglobin of Lupinus Luteus L. With 5 Angstroms Resolution
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1974) Dokl.Biochem.(Engl.Transl.) 216: 226
    • X-Ray Structural Investigation of Leghemoglobin. Vi. Structure of Acetate-Ferrileghemoglobin at a Resolution of 2.0 Angstroms (Russian)
      Arutyunyan, E.G.,Kuranova, I.P.,Vainshtein, B.K.,Steigemann, W.
      (1980) Kristallografiya 25: 80
    • X-Ray Structural Investigation of Leghemoglobin. Iv. Structure Determination at a Resolution of 2.8 Angstroms
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Nekrasov, Yu.V.
      (1978) Sov.Phys.Crystallogr.(Engl.Transl.) 23: 287
    • The X-Ray Structural Study of Leghemoglobin. I. Purification, Crystallization, and Production of Derivatives Containing Heavy Atoms (Russian)
      Vainshtein, B.K.,Arutyunyan, E.G.,Kuranova, I.P.,Borisov, V.V.,Sosfenov, N.I.,Pavlovskii, A.G.,Grebenko, A.I.,Konareva, N.V.
      (1974) Kristallografiya 19: 964
    • Unit-Cell Parameters of Crystalline Plant Hemoglobin
      Arutyunyan, E.G.,Zaitsev, V.N.,Zhiznevskaya, G.Ya.,Borodenko, L.I.
      (1971) Sov.Phys.Crystallogr.(Engl.Transl.) 16: 193


    Organizational Affiliation

    Institute of Crystallography, Russian Academy of Sciences, Moscow.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEGHEMOGLOBIN (DEOXY)
A
153Lupinus luteusN/A
Find proteins for P02240 (Lupinus luteus)
Go to UniProtKB:  P02240
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
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.480α = 90.00
b = 51.600β = 98.80
c = 38.330γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-10-29
    Type: Derived calculations
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other