4LPI

A sperm whale myoglobin double mutant L29H/F43Y Mb with a distal hydrogen-bonding network


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin

Yan, D.J.Yuan, H.Li, W.Xiang, Y.He, B.Nie, C.M.Wen, G.B.Lin, Y.W.Tan, X.

(2015) Dalton Trans 44: 18815-18822

  • DOI: 10.1039/c5dt03040d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of th ...

    A heme-protein cross-link is a key post-translational modification (PTM) of heme proteins. Meanwhile, the structural and functional consequences of heme-protein cross-links are not fully understood, due to limited studies on a direct comparison of the same protein with and without the cross-link. A Tyr-heme cross-link with a C-O bond is a newly discovered PTM of heme proteins, and is spontaneously formed in F43Y myoglobin (Mb) between the Tyr hydroxyl group and the heme 4-vinyl group in vivo. In this study, we found that with an additional distal His29 introduced in the heme pocket, the double mutant L29H/F43Y Mb can form two distinct forms under different protein purification conditions, with and without a novel Tyr-heme cross-link. By solving the X-ray structures of both forms of L29H/F43Y Mb and performing spectroscopic studies, we made a direct structural and functional comparison in the same protein scaffold. It revealed that the Tyr-heme cross-link regulates the heme distal hydrogen-bonding network, and fine-tunes not only the spectroscopic and ligand binding properties, but also the protein reactivity. Moreover, the formation of the Tyr-heme cross-link in the double mutant L29H/F43Y Mb was investigated in vitro. This study addressed the key issue of how Tyr-heme cross-link fine-tunes the structure and functions of the heme protein, and provided a plausible mechanism for the formation of the newly discovered Tyr-heme cross-link.


    Organizational Affiliation

    Department of Chemistry, Tsinghua University, Beijing 100084, China.,Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China. xstan@fudan.edu.cn.,School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. linlinying@hotmail.com ywlin@usc.edu.cn and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.,Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.,School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. linlinying@hotmail.com ywlin@usc.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myoglobin
A
154Physeter macrocephalusMutation(s): 2 
Gene Names: MB
Find proteins for P02185 (Physeter macrocephalus)
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: 1.36 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.884α = 90.00
b = 48.184β = 90.00
c = 78.458γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
PHENIXmodel building
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-07-16 
  • Released Date: 2014-07-16 
  • Deposition Author(s): Lin, Y.

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description