4ZFK | pdb_00004zfk

Ergothioneine-biosynthetic Ntn hydrolase EgtC with glutamine

• PDB DOI: https://doi.org/10.2210/pdb4ZFK/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-04-21 Released: 2015-07-01 
• Deposition Author(s): Vit, A., Seebeck, F.P., Blankenfeldt, W.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Structure of the Ergothioneine-Biosynthesis Amidohydrolase EgtC.

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

(2015) Chembiochem 16: 1490-1496

• PubMed: 26079795 
• DOI: https://doi.org/10.1002/cbic.201500168
• Primary Citation 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.

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Organizational Affiliation: 
• 3Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig (Germany).
Previous address: Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth (Germany).
Department for Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel (Switzerland).
Department for Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel (Switzerland). [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.22 kDa 
• Atom Count: 8,146 
• Modeled Residue Count: 916 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase EgtC	A, B, C, D	235	Mycolicibacterium smegmatis MC2 155	Mutation(s): 4  Gene Names: egtC, MSMEG_6248, MSMEI_6087 EC: 3.5.1 (PDB Primary Data), 3.5.1.118 (UniProt)
UniProt
Find proteins for A0R5M9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R5M9  Go to UniProtKB:  A0R5M9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLN	CA [auth C], I [auth A], IA [auth D], T [auth B]	GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-VKHMYHEASA-N
EDO	AA [auth C], BA [auth C], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.796	α = 90
b = 109.993	β = 90
c = 139.327	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Vit, A., Seebeck, F.P., Blankenfeldt, W.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	147005

Revision History  

• 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
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description