5C6Y | pdb_00005c6y

A sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-heme cross-link

• PDB DOI: https://doi.org/10.2210/pdb5C6Y/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-06-24 Released: 2015-11-11 
• Deposition Author(s): Yuan, H., Lin, Y.W., Tan, X.S.
• Funding Organization(s): National Science Foundation of China, Hunan Provincial Natural Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.181 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

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.S.

(2015) Dalton Trans 44: 18815-18822

• PubMed: 26458300 
• DOI: https://doi.org/10.1039/c5dt03040d
• Primary Citation Related Structures: 
  4LPI, 5C6Y


• 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 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.

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Organizational Affiliation: 
• School of Chemistry and Chemical Engineering, University of South China, Hengyang 421001, China. [e-mail] [e-mail].
Department of Chemistry/Shanghai Key Lab of Chemical Biology for Protein Research & Institute of Biomedical Science, Fudan University, Shanghai 200433, China. [e-mail].
Department of Chemistry, Tsinghua University, Beijing 100084, 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. [e-mail] [e-mail] and Laboratory of Protein Structure and Function, University of South China, Hengyang 421001, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.02 kDa 
• Atom Count: 1,413 
• Modeled Residue Count: 153 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 2  Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	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: 1.79 Å
• R-Value Free:  0.181 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.062	α = 90
b = 48.348	β = 90
c = 79.141	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Yuan, H., Lin, Y.W., Tan, X.S.

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Funding Organization	Location	Grant Number
National Science Foundation of China	China	31370812
National Science Foundation of China	China	31270869
National Science Foundation of China	China	11275090
Hunan Provincial Natural Science Foundation	China	2015JJ1012

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description