3AMO | pdb_00003amo

Time-resolved X-ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase from Arthrobacter globiformis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3AMO

This is version 1.2 of the entry. See complete history

Literature

Detection of the reaction intermediates catalyzed by a copper amine oxidase.

Kataoka, M.Oya, H.Tominaga, A.Otsu, M.Okajima, T.Tanizawa, K.Yamaguchi, H.

(2011) J Synchrotron Radiat 18: 58-61

  • DOI: https://doi.org/10.1107/S0909049510034989
  • Primary Citation Related Structures: 
    3AMO

  • PubMed Abstract: 

    To reveal the chemical changes and geometry changes of active-site residues that cooperate with a reaction is important for understanding the functional mechanism of proteins. Consecutive temporal analyses of enzyme structures have been performed during reactions to clarify structure-based reaction mechanisms. Phenylethylamine oxidase from Arthrobacter globiformis (AGAO) contains a copper ion and topaquinone (TPQ(ox)). The catalytic reaction of AGAO catalyzes oxidative deaminations of phenylethylamine and consists of reductive and oxidative half-reactions. In the reduction step, TPQ(ox) reacts with a phenylethylamine (PEA) substrate giving rise to a topasemiquinone (TPQ(sq)) formed Schiff-base and produces phenylacetaldehyde. To elucidate the mechanism of the reductive half-reaction, an attempt was made to trap the reaction intermediates in order to analyze their structures. The reaction proceeded within the crystals when AGAO crystals were soaked in a PEA solution and freeze-trapped in liquid nitrogen. The reaction stage of each crystal was confirmed by single-crystal microspectrometry, before X-ray diffraction measurements were made of four reaction intermediates. The structure at 15 min after the onset of the reaction was analyzed at atomic resolution, and it was shown that TPQ(ox) and some residues in the substrate channel were alternated via catalytic reductive half-reactions.


  • Organizational Affiliation
    • School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan.

Macromolecule Content 

  • Total Structure Weight: 150.82 kDa 
  • Atom Count: 11,161 
  • Modeled Residue Count: 1,238 
  • Deposited Residue Count: 1,276 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phenylethylamine oxidase638Arthrobacter globiformisMutation(s): 0 
EC: 1.4.3.21
UniProt
Find proteins for P46881 (Arthrobacter globiformis)
Explore P46881 
Go to UniProtKB:  P46881
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46881
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phenylethylamine oxidase638Arthrobacter globiformisMutation(s): 0 
EC: 1.4.3.21
UniProt
Find proteins for P46881 (Arthrobacter globiformis)
Explore P46881 
Go to UniProtKB:  P46881
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46881
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth B]
BA [auth A]
BC [auth B]
CA [auth A]
AA [auth A],
AC [auth B],
BA [auth A],
BC [auth B],
CA [auth A],
CB [auth B],
CC [auth B],
DA [auth A],
DB [auth B],
DC [auth B],
E [auth A],
EA [auth A],
EB [auth B],
EC [auth B],
F [auth A],
FA [auth A],
FB [auth B],
FC [auth B],
G [auth A],
GA [auth A],
GB [auth B],
GC [auth B],
H [auth A],
HA [auth A],
HB [auth B],
HC [auth B],
I [auth A],
IA [auth A],
IB [auth B],
IC [auth B],
J [auth A],
JA [auth A],
JB [auth B],
JC [auth B],
K [auth A],
KA [auth A],
KB [auth B],
KC [auth B],
L [auth A],
LA [auth A],
LB [auth B],
LC [auth B],
M [auth A],
MA [auth A],
MB [auth B],
MC [auth B],
N [auth A],
NA [auth A],
NB [auth B],
NC [auth B],
O [auth A],
OA [auth A],
OB [auth B],
OC [auth B],
P [auth A],
PA [auth A],
PB [auth B],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
Z [auth A],
ZA [auth A],
ZB [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
AB [auth B],
C [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BB [auth B],
D [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
1TY
Query on 1TY
A
L-PEPTIDE LINKINGC17 H18 N2 O4TYR
2TY
Query on 2TY
B
L-PEPTIDE LINKINGC17 H18 N2 O4TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.868α = 90
b = 63.635β = 116.82
c = 157.558γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Refinement description
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary