9ENI | pdb_00009eni

L-amino acid oxidase 4 (HcLAAO4) from the fungus Hebeloma cylindrosporum in complex with L-glutamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and enzyme engineering of the broad substrate spectrum l-amino acid oxidase 4 from the fungus Hebeloma cylindrosporum.

Koopmeiners, S.Gilzer, D.Widmann, C.Berelsmann, N.Spross, J.Niemann, H.H.Fischer von Mollard, G.

(2024) FEBS Lett 598: 2306-2320

  • DOI: https://doi.org/10.1002/1873-3468.15002
  • Primary Citation Related Structures: 
    9ENH, 9ENI, 9ENJ, 9ENK, 9ENN

  • PubMed Abstract: 

    l-Amino acid oxidases (LAAOs) catalyze the oxidative deamination of l-amino acids to α-keto acids. Recombinant production of LAAOs with broad substrate spectrum remains a formidable challenge. We previously achieved this for the highly active and thermostable LAAO4 of Hebeloma cylindrosporum (HcLAAO4). Here, we crystallized a proteolytically truncated surface entropy reduction variant of HcLAAO4 and solved its structure in substrate-free form and in complex with diverse substrates. The ability to support the aliphatic portion of a substrate's side chain by an overall hydrophobic active site is responsible for the broad substrate spectrum of HcLAAO4, including l-amino acids with big aromatic, acidic and basic side chains. Based on the structural findings, we generated an E288H variant with increased activity toward pharmaceutical building blocks of high interest.


  • Organizational Affiliation
    • Biochemistry III, Department of Chemistry, Bielefeld University, Bielefeld, Germany.

Macromolecule Content 

  • Total Structure Weight: 257.76 kDa 
  • Atom Count: 18,620 
  • Modeled Residue Count: 2,135 
  • Deposited Residue Count: 2,248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-amino acid oxidase 4
A, B, C, D
562Hebeloma cylindrosporumMutation(s): 2 
EC: 1.4.3.2 (PDB Primary Data), 1.4.3.25 (UniProt), 1.4.3.11 (UniProt), 1.4.3.14 (UniProt), 1.4.3 (UniProt)
UniProt
Find proteins for S4S6Z0 (Hebeloma cylindrosporum)
Explore S4S6Z0 
Go to UniProtKB:  S4S6Z0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS4S6Z0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDA
(Subject of Investigation/LOI)

Query on FDA



Download:Ideal Coordinates CCD File
DB [auth D],
E [auth A],
OA [auth C],
Y [auth B]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
GLN
(Subject of Investigation/LOI)

Query on GLN



Download:Ideal Coordinates CCD File
EB [auth D],
F [auth A],
PA [auth C],
Z [auth B]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
FB [auth D],
G [auth A],
GA [auth B],
GB [auth D],
H [auth A],
HA [auth B],
HB [auth D],
I [auth A],
IA [auth B],
IB [auth D],
J [auth A],
JA [auth B],
JB [auth D],
K [auth A],
KA [auth B],
KB [auth D],
L [auth A],
LB [auth D],
M [auth A],
MB [auth D],
N [auth A],
NB [auth D],
O [auth A],
OB [auth D],
P [auth A],
PB [auth D],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C],
S [auth A],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C],
ZA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PGO

Query on PGO



Download:Ideal Coordinates CCD File
LA [auth B],
V [auth A]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
PGR

Query on PGR



Download:Ideal Coordinates CCD File
AB [auth C]
BB [auth C]
CB [auth C]
MA [auth B]
NA [auth B]
AB [auth C],
BB [auth C],
CB [auth C],
MA [auth B],
NA [auth B],
QB [auth D],
T [auth A],
U [auth A],
W [auth A],
X [auth A]
R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.71α = 90
b = 131.74β = 95.949
c = 107.25γ = 90
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: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Database references, Structure summary