5HSA | pdb_00005hsa

Alcohol Oxidase AOX1 from Pichia Pastoris

PDB DOI: https://doi.org/10.2210/pdb5HSA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Komagataella phaffii CBS 7435
Expression System: Komagataella phaffii CBS 7435
Mutation(s): No

Deposited: 2016-01-25 Released: 2016-03-09
Deposition Author(s): Neumann, P., Ficner, R., Feussner, I., Koch, C.
Funding Organization(s): German Research Foundation, Goettingen University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.205 (Depositor), 0.207 (DCC)
R-Value Work:
0.177 (Depositor), 0.182 (DCC)
R-Value Observed:
0.179 (Depositor)

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

Crystal Structure of Alcohol Oxidase from Pichia pastoris.

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

(2016) PLoS One 11: e0149846-e0149846

PubMed: 26905908 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0149846
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 602.84 kDa
Atom Count: 44,407
Modeled Residue Count: 5,296
Deposited Residue Count: 5,304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol oxidase 1	A, B, C, D, E A, B, C, D, E, F, G, H	663	Komagataella phaffii CBS 7435	Mutation(s): 0 Gene Names: AOX1, PP7435_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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2QY27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAS Query on FAS Download:Ideal Coordinates CCD File SDF format, chain TA [auth H] SDF format, chain T [auth C] SDF format, chain PA [auth G] SDF format, chain N [auth B] SDF format, chain JA [auth F] SDF format, chain I [auth A] SDF format, chain FA [auth E] SDF format, chain BA [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain PA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain JA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain TA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain PA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain JA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain BA [auth D]	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		Interactions Focus chain BA [auth D] Focus chain FA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain N [auth B] Focus chain PA [auth G] Focus chain T [auth C] Focus chain TA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain FA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain N [auth B] Focus chain PA [auth G] Focus chain T [auth C] Focus chain TA [auth H]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain LA [auth F] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain KA [auth F] SDF format, chain J [auth A] SDF format, chain GA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain LA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain LA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth E]	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		Interactions Focus chain CA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain QA [auth G] SDF format, chain W [auth C] SDF format, chain UA [auth H] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain HA [auth E] SDF format, chain DA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain HA [auth E] MOL2 format, chain DA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain HA [auth E] mmCIF format, chain DA [auth D]	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		Interactions Focus chain DA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain UA [auth H] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain UA [auth H] Focus chain W [auth C]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain MA [auth F] SDF format, chain L [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain L [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain L [auth A]	L [auth A], MA [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth A] Focus chain MA [auth F] Interactions & Density Focus chain L [auth A] Focus chain MA [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain NA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain NA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain NA [auth F]	NA [auth F], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain NA [auth F] Focus chain X [auth C] Interactions & Density Focus chain NA [auth F] Focus chain X [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain SA [auth G] SDF format, chain Z [auth C] SDF format, chain S [auth B] SDF format, chain OA [auth F] SDF format, chain M [auth A] SDF format, chain IA [auth E] SDF format, chain EA [auth D] SDF format, chain AA [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain EA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain EA [auth D] mmCIF format, chain AA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain M [auth A] Focus chain OA [auth F] Focus chain S [auth B] Focus chain SA [auth G] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain M [auth A] Focus chain OA [auth F] Focus chain S [auth B] Focus chain SA [auth G] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain Y [auth C]	Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Y [auth C] Interactions & Density Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.205 (Depositor), 0.207 (DCC)
R-Value Work: 0.177 (Depositor), 0.182 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.1	α = 90
b = 165.19	β = 95.67
c = 164.31	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-03-09

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	IRTG 1422
Goettingen University	Germany	Open 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