5YSN

Ethanolamine ammonia-lyase, AdoCbl/substrate-free


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis.

Shibata, N.Sueyoshi, Y.Higuchi, Y.Toraya, T.

(2018) Angew Chem Int Ed Engl 57: 7830-7835

  • DOI: https://doi.org/10.1002/anie.201803591
  • Primary Citation of Related Structures:  
    5YRT, 5YRV, 5YSH, 5YSN, 5YSR

  • PubMed Abstract: 

    The crystal structures of the B 12 -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.


  • Organizational Affiliation

    Department of Picobiology/Life Science, Graduate School of Life 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 heavy chain
A, C
453Escherichia coli K-12Mutation(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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ethanolamine ammonia-lyase light chain
B, D
295Escherichia coli K-12Mutation(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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12

Download Ideal Coordinates CCD File 
L [auth B],
S [auth D]
COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
5AD
Query on 5AD

Download Ideal Coordinates CCD File 
E [auth A],
M [auth C]
5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.723α = 90
b = 242.723β = 90
c = 76.573γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-09-19 
  • Deposition Author(s): Shibata, N.

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description