9ENJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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

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AA [auth B],
E [auth A],
SB [auth D],
YA [auth C]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
GLU (Subject of Investigation/LOI)
Query on GLU

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BA [auth B],
F [auth A],
TB [auth D],
ZA [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4
Query on SO4

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AB [auth C]
AC [auth D]
BB [auth C]
BC [auth D]
CB [auth C]
AB [auth C],
AC [auth D],
BB [auth C],
BC [auth D],
CB [auth C],
CC [auth D],
DA [auth B],
DB [auth C],
DC [auth D],
EA [auth B],
EB [auth C],
EC [auth D],
FA [auth B],
FB [auth C],
G [auth A],
GA [auth B],
GB [auth C],
H [auth A],
HA [auth B],
HB [auth C],
I [auth A],
IA [auth B],
IB [auth C],
J [auth A],
JA [auth B],
JB [auth C],
K [auth A],
KA [auth B],
KB [auth C],
L [auth A],
LA [auth B],
LB [auth C],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
UB [auth D],
VB [auth D],
WB [auth D],
XB [auth D],
YB [auth D],
ZB [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PGR
Query on PGR

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FC [auth D]
JC [auth D]
KC [auth D]
MB [auth C]
OB [auth C]
FC [auth D],
JC [auth D],
KC [auth D],
MB [auth C],
OB [auth C],
QB [auth C],
RB [auth D],
SA [auth B],
T [auth A],
WA [auth B],
X [auth A],
Z [auth A]
R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
PGO
Query on PGO

Download Ideal Coordinates CCD File 
CA [auth B]
GC [auth D]
HC [auth D]
IC [auth D]
NB [auth C]
CA [auth B],
GC [auth D],
HC [auth D],
IC [auth D],
NB [auth C],
PB [auth C],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
XA [auth B],
Y [auth A]
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.76α = 90
b = 130.79β = 95.655
c = 107.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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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