5YZF

X-ray crystal structure of met K42C sperm whale myoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen

Cheng, H.M.Yuan, H.Wang, X.J.Xu, J.K.Gao, S.Q.Wen, G.B.Tan, X.Lin, Y.W.

(2018) J. Inorg. Biochem. 182: 141-149

  • DOI: 10.1016/j.jinorgbio.2018.02.011

  • PubMed Abstract: 
  • The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme ...

    The structure and function of heme proteins are regulated by diverse post-translational modifications including heme-protein cross-links, with the underlying mechanisms not well understood. In this study, we introduced a Cys (K42C) close to the heme 4-vinyl group in sperm whale myoglobin (Mb) and solved its X-ray crystal structure. Interestingly, we found that K42C Mb can partially form a Cys-heme cross-link (termed K42C Mb-X) under dithiothreitol-induced reductive conditions in presence of O 2 , as suggested by guanidine hydrochloride-induced unfolding and heme extraction studies. Mass spectrometry (MS) studies, together with trypsin digestion studies, further indicated that a thioether bond is formed between Cys42 and the heme 4-vinyl group with an additional mass of 16 Da, likely due to hydroxylation of the α‑carbon. We then proposed a plausible mechanism for the formation of the novel Cys-heme cross-link based on MS, kinetic UV-vis and electron paramagnetic resonance (EPR) studies. Moreover, the Cys-heme cross-link was shown to fine-tune the protein reactivity toward activation of H 2 O 2 . This study provides valuable insights into the post-translational modification of heme proteins, and also suggests that the Cys-heme cross-link can be induced to form in vitro, making it useful for design of new heme proteins with a non-dissociable heme and improved functions.


    Organizational Affiliation

    Department of Chemistry, Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China.,School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.,Yellow Sea Fisheries Research Institute, Qingdao 266071, China.,Lab 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; Lab of Protein Structure and Function, University of South China, Hengyang 421001, China. Electronic address: ywlin@usc.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
sperm whale myoglobin
A
154Physeter macrocephalusMutation(s): 1 
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: 1.77 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.794α = 90.00
b = 47.931β = 90.00
c = 82.705γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
MOLREPphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-14 
  • Released Date: 2018-03-07 
  • Deposition Author(s): Yuan, H.

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release