5YZF | pdb_00005yzf

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 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5YZF

Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1016/j.jinorgbio.2018.02.011
  • Primary Citation Related Structures: 
    5YZF

  • 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 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
    • School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China.

Macromolecule Content 

  • Total Structure Weight: 17.96 kDa 
  • Atom Count: 1,467 
  • Modeled Residue Count: 154 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
sperm whale myoglobin154Physeter macrocephalusMutation(s): 1 
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.203 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.794α = 90
b = 47.931β = 90
c = 82.705γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description