3ABQ

Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and 2-amino-1-propanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates.

Shibata, N.Tamagaki, H.Hieda, N.Akita, K.Komori, H.Shomura, Y.Terawaki, S.Mori, K.Yasuoka, N.Higuchi, Y.Toraya, T.

(2010) J.Biol.Chem. 285: 26484-26493

  • DOI: 10.1074/jbc.M110.125112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase beta-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Tor ...

    N-terminal truncation of the Escherichia coli ethanolamine ammonia-lyase beta-subunit does not affect the catalytic properties of the enzyme (Akita, K., Hieda, N., Baba, N., Kawaguchi, S., Sakamoto, H., Nakanishi, Y., Yamanishi, M., Mori, K., and Toraya, T. (2010) J. Biochem. 147, 83-93). The binary complex of the truncated enzyme with cyanocobalamin and the ternary complex with cyanocobalamin or adeninylpentylcobalamin and substrates were crystallized, and their x-ray structures were analyzed. The enzyme exists as a trimer of the (alphabeta)(2) dimer. The active site is in the (beta/alpha)(8) barrel of the alpha-subunit; the beta-subunit covers the lower part of the cobalamin that is bound in the interface of the alpha- and beta-subunits. The structure complexed with adeninylpentylcobalamin revealed the presence of an adenine ring-binding pocket in the enzyme that accommodates the adenine moiety through a hydrogen bond network. The substrate is bound by six hydrogen bonds with active-site residues. Argalpha(160) contributes to substrate binding most likely by hydrogen bonding with the O1 atom. The modeling study implies that marked angular strains and tensile forces induced by tight enzyme-coenzyme interactions are responsible for breaking the coenzyme Co-C bond. The coenzyme adenosyl radical in the productive conformation was modeled by superimposing its adenine ring on the adenine ring-binding site followed by ribosyl rotation around the N-glycosidic bond. A major structural change upon substrate binding was not observed with this particular enzyme. Glualpha(287), one of the substrate-binding residues, has a direct contact with the ribose group of the modeled adenosylcobalamin, which may contribute to the substrate-induced additional labilization of the Co-C bond.


    Organizational Affiliation

    Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan. shibach@sci.u-hyogo.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ethanolamine ammonia-lyase heavy chain
A, C
453Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: eutB
EC: 4.3.1.7
Find proteins for P0AEJ6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEJ6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ethanolamine ammonia-lyase light chain
B, D
306Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: eutC
EC: 4.3.1.7
Find proteins for P19636 (Escherichia coli (strain K12))
Go to UniProtKB:  P19636
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2A1
Query on 2A1

Download SDF File 
Download CCD File 
A, C
(2S)-2-aminopropan-1-ol
C3 H9 N O
BKMMTJMQCTUHRP-VKHMYHEASA-N
 Ligand Interaction
B12
Query on B12

Download SDF File 
Download CCD File 
B, D
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 241.870α = 90.00
b = 241.870β = 90.00
c = 76.290γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-12-21 
  • Released Date: 2010-06-02 
  • Deposition Author(s): Shibata, N.

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-10-24
    Type: Non-polymer description
  • Version 1.3: 2014-02-19
    Type: Database references, Derived calculations