4ZFJ

Ergothioneine-biosynthetic Ntn hydrolase EgtC, apo form

PDB DOI: https://doi.org/10.2210/pdb4ZFJ/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.180
R-Value Work: 0.149
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 26079795 Search on PubMed
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).

Macromolecule Content

Total Structure Weight: 310.49 kDa
Atom Count: 23,369
Modelled Residue Count: 2,732
Deposited Residue Count: 2,820
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase EgtC	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	235	Mycolicibacterium smegmatis MC2 155	Mutation(s): 6 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R5M9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XPE Query on XPE Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain EA [auth J] SDF format, chain GA [auth K] SDF format, chain IA [auth L] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain IA [auth L] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth G] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain GA [auth K] mmCIF format, chain IA [auth L] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth G]	AA [auth H] CA [auth I] EA [auth J] GA [auth K] IA [auth L] AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], P [auth B], Q [auth C], S [auth D], T [auth D], V [auth E], Y [auth G]	3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL C₂₀ H₄₂ O₁₁ DTPCFIHYWYONMD-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain Y [auth G]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain FA [auth K] SDF format, chain HA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain HA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain HA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	BA [auth I] DA [auth J] FA [auth K] HA [auth L] M [auth A] BA [auth I], DA [auth J], FA [auth K], HA [auth L], M [auth A], N [auth A], O [auth B], R [auth D], U [auth E], W [auth F], X [auth G], Z [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain FA [auth K] Focus chain HA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain R [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Z [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.180
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.977	α = 90
b = 69.507	β = 94.84
c = 160.375	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

Vit, A.

Seebeck, F.P.

Blankenfeldt, W.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	147005

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: 2017-10-18
Changes: Data collection

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Help and Resources

4ZFJ

Ergothioneine-biosynthetic Ntn hydrolase EgtC, apo form

Structure of the Ergothioneine-Biosynthesis Amidohydrolase EgtC.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)