7XRM

Ethanolamine ammonia-lyase complexed with AdoMeCbl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into the Very Low Activity of the Homocoenzyme B 12 Adenosylmethylcobalamin in Coenzyme B 12 -Dependent Diol Dehydratase and Ethanolamine Ammonia-Lyase.

Shibata, N.Higuchi, Y.Krautler, B.Toraya, T.

(2022) Chemistry 28: e202202196-e202202196

  • DOI: https://doi.org/10.1002/chem.202202196
  • Primary Citation of Related Structures:  
    7XRK, 7XRL, 7XRM, 7XRN

  • PubMed Abstract: 

    The X-ray structures of coenzyme B 12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. As judged from geometries, the Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate; in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The impacts of incorporating an extra CH 2 group are different in the two enzymes: the DD active site is flexible, and AdoMeCbl binding causes large conformational changes that make DD unable to adopt the catalytic state, whereas the EAL active site is rigid, and AdoMeCbl binding does not induce significant conformational changes. Such flexibility and rigidity of the active sites might reflect the tightness of adenine binding. The structures provide good insights into the basis of the very low activity of AdoMeCbl in these enzymes.


  • Organizational Affiliation

    Department of Life Science, Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine ammonia-lyase large subunit
A, C
453Escherichia coliMutation(s): 0 
Gene Names: eutBb2441JW2434
EC: 4.3.1.7
UniProt
Find proteins for P0AEJ6 (Escherichia coli (strain K12))
Explore P0AEJ6 
Go to UniProtKB:  P0AEJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEJ6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine ammonia-lyase small subunit
B, D
263Escherichia coliMutation(s): 0 
Gene Names: eutCb2440JW2433
EC: 4.3.1.7
UniProt
Find proteins for P19636 (Escherichia coli (strain K12))
Explore P19636 
Go to UniProtKB:  P19636
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19636
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
K [auth B],
U [auth D]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
FWK (Subject of Investigation/LOI)
Query on FWK

Download Ideal Coordinates CCD File 
J [auth A],
T [auth C]
(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol
C11 H15 N5 O3
RLOSCLOIJYLPHI-IOSLPCCCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth C]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
I [auth A],
S [auth C]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.885α = 90
b = 242.885β = 90
c = 76.638γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description