4ZFL

Ergothioneine-biosynthetic Ntn hydrolase variant EgtC_C2A with natural substrate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Structure of the Ergothioneine-Biosynthesis Amidohydrolase EgtC.

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

(2015) Chembiochem 16: 1490-1496

  • DOI: 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 ...

    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: 

    Department for Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel (Switzerland). florian.seebeck@unibas.ch.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amidohydrolase EgtC
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
234Mycolicibacterium smegmatis MC2 155Mutation(s): 5 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R5M9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NK
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]
(1S)-1-carboxy-4-({(1R)-1-carboxy-2-[(S)-{4-[(2S)-2-carboxy-2-(trimethylammonio)ethyl]-1H-imidazol-2-yl}sulfinyl]ethyl}amino)-4-oxobutan-1-aminium
C17 H29 N5 O8 S
SJHLSLUUWIBQNS-HBCRSHFUSA-P		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth K],
R [auth E],
U [auth G],
X [auth I]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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