4E2X

X-ray Structure of the Y222F mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and dTDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose.

Bruender, N.A.Holden, H.M.

(2012) Protein Sci 21: 876-886

  • DOI: 10.1002/pro.2074
  • Primary Citation of Related Structures:  
    4E2Y, 4E2Z, 4E32, 4E33, 4E2W, 4E2X, 4E30, 4E31

  • PubMed Abstract: 
  • D-Tetronitrose is a nitro-containing tetradeoxysugar found attached to the antitumor and antibacterial agent tetrocarcin A. The biosynthesis of this highly unusual sugar in Micromonospora chalcea requires 10 enzymes. The fifth step in the pathway inv ...

    D-Tetronitrose is a nitro-containing tetradeoxysugar found attached to the antitumor and antibacterial agent tetrocarcin A. The biosynthesis of this highly unusual sugar in Micromonospora chalcea requires 10 enzymes. The fifth step in the pathway involves the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to the C-3' carbon of dTDP-3-amino-2,3,6-trideoxy-4-keto-D-glucose. The enzyme responsible for this transformation is referred to as TcaB9. It is a monomeric enzyme with a molecular architecture based around three domains. The N-terminal motif contains a binding site for a structural zinc ion. The middle- and C-terminal domains serve to anchor the SAM and dTDP-sugar ligands, respectively, to the protein, and the active site of TcaB9 is wedged between these two regions. For this investigation, the roles of Tyr 76, His 181, Tyr 222, Glu 224, and His 225, which form the active site of TcaB9, were probed by site-directed mutagenesis, kinetic analyses, and X-ray structural studies. In addition, two ternary complexes of the enzyme with bound S-adenosyl-L-homocysteine and either dTDP-3-amino-2,3,6-trideoxy-4-keto-D-glucose or dTDP-3-amino-2,3,6-trideoxy-D-galactose were determined to 1.5 or 1.6 Å resolution, respectively. Taken together, these investigations highlight the important role of His 225 in methyl transfer. In addition, the structural data suggest that the methylation reaction occurs via retention of configuration about the C-3' carbon of the sugar.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TcaB9A416Micromonospora chalceaMutation(s): 1 
Gene Names: tcab9
EC: 2.1.1
Find proteins for B5L6K6 (Micromonospora chalcea)
Explore B5L6K6 
Go to UniProtKB:  B5L6K6
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYD
Query on TYD

Download CCD File 
A
THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
 Ligand Interaction
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.542α = 90
b = 114.174β = 90
c = 37.632γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references