4P8I

Tgl - a bacterial spore coat transglutaminase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking.

Fernandes, C.G.Placido, D.Lousa, D.Brito, J.A.Isidro, A.Soares, C.M.Pohl, J.Carrondo, M.A.Archer, M.Henriques, A.O.

(2015) Biochemistry 54: 5723-5734

  • DOI: https://doi.org/10.1021/acs.biochem.5b00661
  • Primary Citation of Related Structures:  
    4P8I, 4PA5

  • PubMed Abstract: 

    Transglutaminases are best known for their ability to catalyze protein cross-linking reactions that impart chemical and physical resilience to cellular structures. Here, we report the crystal structure and characterization of Tgl, a transglutaminase from the bacterium Bacillus subtilis. Tgl is produced during sporulation and cross-links the surface of the highly resilient spore. Tgl-like proteins are found only in spore-forming bacteria of the Bacillus and Clostridia classes, indicating an ancient origin. Tgl is a single-domain protein, produced in active form, and the smallest transglutaminase characterized to date. We show that Tgl is structurally similar to bacterial cell wall endopeptidases and has an NlpC/P60 catalytic core, thought to represent the ancestral unit of the cysteine protease fold. We show that Tgl functions through a unique partially redundant catalytic dyad formed by Cys116 and Glu187 or Glu115. Strikingly, the catalytic Cys is insulated within a hydrophobic tunnel that traverses the molecule from side to side. The lack of similarity of Tgl to other transglutaminases together with its small size suggests that an NlpC/P60 catalytic core and insulation of the active site during catalysis may be essential requirements for protein cross-linking.


  • Organizational Affiliation

    Biotechnology Branch, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-glutamine gamma-glutamyltransferase
A, B
260Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: tglyugVyuxFBSU31270
EC: 2.3.2.13
UniProt
Find proteins for P40746 (Bacillus subtilis (strain 168))
Explore P40746 
Go to UniProtKB:  P40746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40746
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.158 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.94α = 90
b = 97.94β = 90
c = 66.183γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SHARPphasing
BUSTER-TNTrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundao para a Cincia e a TecnologiaPortugalPOCI/BIA-BCM/60855/2004
Fundao para a Cincia e a TecnologiaPortugalPOCTI/BCI/48647/2002
Fundao para a Cincia e a TecnologiaPortugalPTDC/SAU-NEU/103720/2008

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references