5HSA

Alcohol Oxidase AOX1 from Pichia Pastoris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Alcohol Oxidase from Pichia pastoris.

Koch, C.Neumann, P.Valerius, O.Feussner, I.Ficner, R.

(2016) PLoS One 11: e0149846-e0149846

  • DOI: https://doi.org/10.1371/journal.pone.0149846
  • Primary Citation of Related Structures:  
    5HSA

  • PubMed Abstract: 

    FAD-dependent alcohol oxidases (AOX) are key enzymes of methylotrophic organisms that can utilize lower primary alcohols as sole source of carbon and energy. Here we report the crystal structure analysis of the methanol oxidase AOX1 from Pichia pastoris. The crystallographic phase problem was solved by means of Molecular Replacement in combination with initial structure rebuilding using Rosetta model completion and relaxation against an averaged electron density map. The subunit arrangement of the homo-octameric AOX1 differs from that of octameric vanillyl alcohol oxidase and other dimeric or tetrameric alcohol oxidases, due to the insertion of two large protruding loop regions and an additional C-terminal extension in AOX1. In comparison to other alcohol oxidases, the active site cavity of AOX1 is significantly reduced in size, which could explain the observed preference for methanol as substrate. All AOX1 subunits of the structure reported here harbor a modified flavin adenine dinucleotide, which contains an arabityl chain instead of a ribityl chain attached to the isoalloxazine ring.


  • Organizational Affiliation

    Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol oxidase 1
A, B, C, D, E
A, B, C, D, E, F, G, H
663Komagataella phaffii CBS 7435Mutation(s): 0 
Gene Names: AOX1PP7435_Chr4-0130
EC: 1.1.3.13
UniProt
Find proteins for F2QY27 (Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
Explore F2QY27 
Go to UniProtKB:  F2QY27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2QY27
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAS
Query on FAS

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth E]
I [auth A]
JA [auth F]
N [auth B]
BA [auth D],
FA [auth E],
I [auth A],
JA [auth F],
N [auth B],
PA [auth G],
T [auth C],
TA [auth H]
ARABINO-FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-WCVIGVMNSA-N
P6G
Query on P6G

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CA [auth D]
GA [auth E]
J [auth A]
KA [auth F]
LA [auth F]
CA [auth D],
GA [auth E],
J [auth A],
KA [auth F],
LA [auth F],
O [auth B],
P [auth B],
U [auth C],
V [auth C]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE
Query on PGE

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DA [auth D]
HA [auth E]
K [auth A]
Q [auth B]
QA [auth G]
DA [auth D],
HA [auth E],
K [auth A],
Q [auth B],
QA [auth G],
R [auth B],
RA [auth G],
UA [auth H],
W [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4
Query on PO4

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L [auth A],
MA [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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NA [auth F],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

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AA [auth C]
EA [auth D]
IA [auth E]
M [auth A]
OA [auth F]
AA [auth C],
EA [auth D],
IA [auth E],
M [auth A],
OA [auth F],
S [auth B],
SA [auth G],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
Y [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.1α = 90
b = 165.19β = 95.67
c = 164.31γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyIRTG 1422
Goettingen UniversityGermanyOpen Access Publication Funds

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description