5M6Q

Crystal Structure of Kutzneria albida transglutaminase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of a microbial transglutaminase enabling highly site-specific labeling of proteins.

Steffen, W.Ko, F.C.Patel, J.Lyamichev, V.Albert, T.J.Benz, J.Rudolph, M.G.Bergmann, F.Streidl, T.Kratzsch, P.Boenitz-Dulat, M.Oelschlaegel, T.Schraeml, M.

(2017) J Biol Chem 292: 15622-15635

  • DOI: https://doi.org/10.1074/jbc.M117.797811
  • Primary Citation of Related Structures:  
    5M6Q

  • PubMed Abstract: 

    Microbial transglutaminases (MTGs) catalyze the formation of Gln-Lys isopeptide bonds and are widely used for the cross-linking of proteins and peptides in food and biotechnological applications ( e.g. to improve the texture of protein-rich foods or in generating antibody-drug conjugates). Currently used MTGs have low substrate specificity, impeding their biotechnological use as enzymes that do not cross-react with nontarget substrates ( i.e. as bio-orthogonal labeling systems). Here, we report the discovery of an MTG from Kutzneria albida (KalbTG), which exhibited no cross-reactivity with known MTG substrates or commonly used target proteins, such as antibodies. KalbTG was produced in Escherichia coli as soluble and active enzyme in the presence of its natural inhibitor ammonium to prevent potentially toxic cross-linking activity. The crystal structure of KalbTG revealed a conserved core similar to other MTGs but very short surface loops, making it the smallest MTG characterized to date. Ultra-dense peptide array technology involving a pool of 1.4 million unique peptides identified specific recognition motifs for KalbTG in these peptides. We determined that the motifs YRYRQ and RYESK are the best Gln and Lys substrates of KalbTG, respectively. By first reacting a bifunctionalized peptide with the more specific KalbTG and in a second step with the less specific MTG from Streptomyces mobaraensis , a successful bio-orthogonal labeling system was demonstrated. Fusing the KalbTG recognition motif to an antibody allowed for site-specific and ratio-controlled labeling using low label excess. Its site specificity, favorable kinetics, ease of use, and cost-effective production render KalbTG an attractive tool for a broad range of applications, including production of therapeutic antibody-drug conjugates.


  • Organizational Affiliation

    From Roche Diagnostics GmbH, CPS, Nonnenwald 2, 82377 Penzberg, Germany, wojtek.steffen@roche.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
225Kutzneria albida DSM 43870Mutation(s): 0 
Gene Names: KALB_7456
UniProt
Find proteins for W5WHY8 (Kutzneria albida DSM 43870)
Explore W5WHY8 
Go to UniProtKB:  W5WHY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5WHY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.87α = 90
b = 106.87β = 90
c = 56.08γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description