1IOP

INCORPORATION OF A HEMIN WITH THE SHORTEST ACID SIDE-CHAINS INTO MYOGLOBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and function of 6,7-dicarboxyheme-substituted myoglobin

Neya, S.Funasaki, N.Igarashi, N.Ikezaki, A.Sato, T.Imai, K.Tanaka, N.

(1998) Biochemistry 37: 5487-5493

  • DOI: 10.1021/bi972632c
  • Primary Citation of Related Structures:  
    1IOP

  • PubMed Abstract: 
  • Myoglobin was reconstituted with 6,7-dicarboxy-1,2,3,4,5, 8-hexamethylheme, a compact synthetic heme with the shortest acid side chains, to pursue the structural and functional consequences after intensive disruption of the heme propionate-apoglobin ...

    Myoglobin was reconstituted with 6,7-dicarboxy-1,2,3,4,5, 8-hexamethylheme, a compact synthetic heme with the shortest acid side chains, to pursue the structural and functional consequences after intensive disruption of the heme propionate-apoglobin linkages in the native protein. The electron-withdrawing carboxylate groups directly attached to the porphyrin ring lowered the oxygen affinity by 3-fold as compared with native myoglobin. Autoxidation of the oxy derivative to the ferric protein proceeded with 1.6 x 10(-)2 min-1 at pH 7.0 and 30 degrees C. The crystallographic structure of the cyanomet myoglobin with 1.9 A resolution shows that the heme adopts a unique orientation in the protein pocket to extend the two carboxylates toward solvent sphere. The native globin fold is conserved, and the conformations of globin side chains are almost intact except for those located nearby the heme 6,7-carboxylates. The 7-carboxylate only weakly interacts with Ser92 and His97 through two mediating water molecules. The 6-carboxylate, on the other hand, forms a novel salt bridge with Arg45 owing to conformational flexibility of the guanidinium side chain. The proton NMR shows that the small heme does not fluctuate about the iron-histidine bond even at 55 degreesC, suggesting that the salt bridge between Arg45 and heme 6-carboxylate is of critical importance to recognize and fix the heme in myoglobin.


    Organizational Affiliation

    Department of Physical Chemistry, Kyoto Pharmaceutical University, Japan. sneya@mb.kyoto-phu.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MYOGLOBINA153Physeter catodonMutation(s): 0 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HE6
Query on HE6

Download CCD File 
A
6,7-DICARBOXYL-1,2,3,4,5,8-HEXAMETHYLHEMIN
C28 H24 Fe N4 O4
RFDMLTBFXDEWRD-MAUQWHLVDC
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CYN
Query on CYN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.02α = 90
b = 91.02β = 90
c = 45.68γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance