9JQD

Cryo-EM structure of ferritin variant R63MeH/R67MeH

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

  • Deposited: 2024-09-27 Released: 2024-11-27 
  • Deposition Author(s): Wang, C.H., Wang, Y.S.
  • Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan), National Science Council (NSC, Taiwan)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Site-Specific Histidine Aza-Michael Addition in Proteins Enabled by a Ferritin-Based Metalloenzyme.

Tsou, J.C.Tsou, C.J.Wang, C.H.Ko, A.A.Wang, Y.H.Liang, H.H.Sun, J.C.Huang, K.F.Ko, T.P.Lin, S.Y.Wang, Y.S.

(2024) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.4c14446
  • Primary Citation of Related Structures:  
    9JIU, 9JQB, 9JQC, 9JQD, 9JQE

  • PubMed Abstract: 

    Histidine modifications of proteins are broadly based on chemical methods triggering N-substitution reactions such as aza-Michael addition at histidine's moderately nucleophilic imidazole side chain. While recent studies have demonstrated chemoselective, histidine-specific modifications by further exploiting imidazole's electrophilic reactivity to overcome interference from the more nucleophilic lysine and cysteine, achieving site-specific histidine modifications remains a major challenge due to the absence of spatial control over chemical processes. Herein, through X-ray crystallography and cryo-electron microscopy structural studies, we describe the rational design of a nature-inspired, noncanonical amino-acid-incorporated, human ferritin-based metalloenzyme that is capable of introducing site-specific post-translational modifications (PTMs) to histidine in peptides and proteins. Specifically, chemoenzymatic aza-Michael additions on single histidine residues were carried out on eight protein substrates ranging from 10 to 607 amino acids including the insulin peptide hormone. By introducing an insulin-targeting peptide into our metalloenzyme, we further directed modifications to be carried out site-specifically on insulin's B-chain histidine 5. The success of this biocatalysis platform outlines a novel approach in introducing residue- and, moreover, site-specific post-translational modifications to peptides and proteins, which may further enable reactions to be carried out in vivo .


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin heavy chain
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
183Homo sapiensMutation(s): 2 
Gene Names: FTH1FTHFTHL6OK/SW-cl.84PIG15
EC: 1.16.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P02794 (Homo sapiens)
Explore P02794 
Go to UniProtKB:  P02794
PHAROS:  P02794
GTEx:  ENSG00000167996 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02794
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth O]
BA [auth B]
BB [auth O]
CA [auth C]
AA [auth B],
AB [auth O],
BA [auth B],
BB [auth O],
CA [auth C],
CB [auth P],
DA [auth C],
DB [auth P],
EA [auth D],
EB [auth Q],
FA [auth D],
FB [auth Q],
GA [auth E],
GB [auth R],
HA [auth E],
HB [auth R],
IA [auth F],
IB [auth S],
JA [auth F],
JB [auth S],
KA [auth G],
KB [auth T],
LA [auth G],
LB [auth T],
MA [auth H],
MB [auth U],
NA [auth H],
NB [auth U],
OA [auth I],
OB [auth V],
PA [auth I],
PB [auth V],
QA [auth J],
QB [auth W],
RA [auth J],
RB [auth W],
SA [auth K],
SB [auth X],
TA [auth K],
TB [auth X],
UA [auth L],
VA [auth L],
WA [auth M],
XA [auth M],
Y [auth A],
YA [auth N],
Z [auth A],
ZA [auth N]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MHS
Query on MHS
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--
Ministry of Science and Technology (MoST, Taiwan)Taiwan107-2113-M-001-025-MY3
National Science Council (NSC, Taiwan)Taiwan113-2113-M-001 -006 -

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release