4ZOH

Crystal structure of glyceraldehyde oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Archaeal Mo-Containing Glyceraldehyde Oxidoreductase Isozymes Exhibit Diverse Substrate Specificities through Unique Subunit Assemblies.

Wakagi, T.Nishimasu, H.Miyake, M.Fushinobu, S.

(2016) PLoS One 11: e0147333-e0147333

  • DOI: https://doi.org/10.1371/journal.pone.0147333
  • Primary Citation of Related Structures:  
    4ZOH

  • PubMed Abstract: 

    Archaea use glycolytic pathways distinct from those found in bacteria and eukaryotes, where unique enzymes catalyze each reaction step. In this study, we isolated three isozymes of glyceraldehyde oxidoreductase (GAOR1, GAOR2 and GAOR3) from the thermoacidophilic archaeon Sulfolobus tokodaii. GAOR1-3 belong to the xanthine oxidoreductase superfamily, and are composed of a molybdo-pyranopterin subunit (L), a flavin subunit (M), and an iron-sulfur subunit (S), forming an LMS hetero-trimer unit. We found that GAOR1 is a tetramer of the STK17810/STK17830/STK17820 hetero-trimer, GAOR2 is a dimer of the STK23390/STK05620/STK05610 hetero-trimer, and GAOR3 is the STK24840/STK05620/STK05610 hetero-trimer. GAOR1-3 exhibited diverse substrate specificities for their electron donors and acceptors, due to their different L-subunits, and probably participate in the non-phosphorylative Entner-Doudoroff glycolytic pathway. We determined the crystal structure of GAOR2, as the first three-dimensional structure of an archaeal molybdenum-containing hydroxylase, to obtain structural insights into their substrate specificities and subunit assemblies. The gene arrangement and the crystal structure suggested that the M/S-complex serves as a structural scaffold for the binding of the L-subunit, to construct the three enzymes with different specificities. Collectively, our findings illustrate a novel principle of a prokaryotic multicomponent isozyme system.


  • Organizational Affiliation

    Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative oxidoreductase molybdopterin-binding subunit706Sulfurisphaera tokodaii str. 7Mutation(s): 0 
UniProt
Find proteins for Q96Y29 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q96Y29 
Go to UniProtKB:  Q96Y29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96Y29
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative oxidoreductase FAD-binding subunit278Sulfurisphaera tokodaii str. 7Mutation(s): 0 
UniProt
Find proteins for Q974U9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q974U9 
Go to UniProtKB:  Q974U9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ974U9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative oxidoreductase iron-sulfur subunit168Sulfurisphaera tokodaii str. 7Mutation(s): 0 
UniProt
Find proteins for Q974V0 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q974V0 
Go to UniProtKB:  Q974V0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ974V0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
H [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MCN
Query on MCN

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D [auth A]PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
1PE
Query on 1PE

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F [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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J [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
FES
Query on FES

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M [auth C],
N [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
PEG
Query on PEG

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G [auth A],
I [auth B],
K [auth B],
O [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MO
Query on MO

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E [auth A]MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
ACY
Query on ACY

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L [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.431α = 90
b = 143.431β = 90
c = 235.509γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
ARPmodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KakenhiJapan24580136
JSPS KakenhiJapan18580088
JSPS KakenhiJapan12660067

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description