Ergothioneine-biosynthetic Ntn hydrolase variant EgtC_C2A with natural substrate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure of the Ergothioneine-Biosynthesis Amidohydrolase EgtC.

Vit, A.Mashabela, G.T.Blankenfeldt, W.Seebeck, F.P.

(2015) Chembiochem 16: 1490-1496

  • DOI: https://doi.org/10.1002/cbic.201500168
  • Primary Citation of Related Structures:  
    4ZFJ, 4ZFK, 4ZFL

  • PubMed Abstract: 

    The ubiquitous sulfur metabolite ergothioneine is biosynthesized by oxidative attachment of a sulfur atom to the imidazole ring of Nα-trimethylhistidine. Most actinobacteria, including Mycobacterium tuberculosis, use γ-glutamyl cysteine as a sulfur donor. In subsequent steps the carbon scaffold of γ-glutamyl cysteine is removed by the glutamine amidohydrolase EgtC and the β-lyase EgtE. We determined the crystal structure of EgtC from Mycobacterium smegmatis in complex with its physiological substrate. The set of active site residues that define substrate specificity in EgtC are highly conserved, even in homologues that are not involved in ergothioneine production. This conservation is compounded by the phylogenetic distribution of EgtC-like enzymes indicates that their last common ancestor might have emerged for a purpose other than ergothioneine production.

  • Organizational Affiliation

    3Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig (Germany).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amidohydrolase EgtC
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
234Mycolicibacterium smegmatis MC2 155Mutation(s): 5 
Gene Names: egtCMSMEG_6248MSMEI_6087
EC: 3.5.1
Find proteins for A0R5M9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R5M9 
Go to UniProtKB:  A0R5M9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R5M9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4NK

Download Ideal Coordinates CCD File 
BA [auth L]
M [auth A]
N [auth B]
O [auth C]
P [auth D]
BA [auth L],
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
S [auth F],
T [auth G],
V [auth H],
W [auth I],
Y [auth J],
Z [auth K]
C17 H29 N5 O8 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth K],
R [auth E],
U [auth G],
X [auth I]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.47α = 90
b = 69.363β = 94.67
c = 159.408γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland147005

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description