6JT5

Crystal structure of PQQ doamin of Pyranose Dehydrogenase from Coprinopsis cinerea: apo-from


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.105 

wwPDB Validation 3D Report Full Report


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Literature

The Crystal Structure of the Catalytic Domain and the CytochromebDomain in a Eukaryotic PQQ-Dependent Dehydrogenase.

Takeda, K.Ishida, T.Yoshida, M.Samejima, M.Ohno, H.Igarashi, K.Nakamura, N.

(2019) Appl.Environ.Microbiol. --: --

  • DOI: 10.1128/AEM.01692-19
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyrroloquinoline quinone (PQQ) was discovered as a redox cofactor of prokaryotic glucose dehydrogenases in the 1960s, and subsequent studies have demonstrated its importance not only in bacterial systems but also in higher organisms. We have previous ...

    Pyrroloquinoline quinone (PQQ) was discovered as a redox cofactor of prokaryotic glucose dehydrogenases in the 1960s, and subsequent studies have demonstrated its importance not only in bacterial systems but also in higher organisms. We have previously reported a novel eukaryotic quinohemoprotein that exhibited PQQ-dependent catalytic activity in a eukaryote. The enzyme, pyranose dehydrogenase, from the filamentous fungus Coprinopsis cinerea ( Cc PDH) of the Basidiomycete division, is composed of a catalytic PQQ-dependent domain classified as a member of the novel auxiliary activity family 12 (AA12), an AA8 cytochrome b domain, and a family 1 carbohydrate-binding module (CBM1), as defined by the Carbohydrate-Active enZymes (CAZy) database. Here, we present crystal structures of the AA12 domain in its apo and holo forms and the AA8 domain of this enzyme. The crystal structures of the holo-AA12 domain bound to PQQ provide direct evidence that eukaryotes have PQQ-dependent enzymes. The AA12 domain exhibits a six-bladed β-propeller fold that is also present in other known PQQ-dependent glucose dehydrogenases in bacteria. A loop structure around the active site and a calcium ion binding site are unique among the known structures of bacterial quinoproteins. The AA8 cytochrome domain has a positively charged area on its molecular surface, which is partly due to the propionate group of the heme interacting with Arg181; this feature differs from that of cytochrome b in the AA8 domain of the fungal cellobiose dehydrogenase and suggests that this difference may affect the pH dependence of electron transfer. Importance Pyrroloquinoline quinone (PQQ) is known as the "third coenzyme" following nicotinamide adenine dinucleotide (NAD + ) and flavin adenine dinucleotide (FAD). PQQ-dependent enzymes have been previously found only in prokaryotes, and the existence of a eukaryotic PQQ-dependent enzyme was in doubt. In 2014, we found an enzyme in mushrooms that catalyzes the oxidation of various sugars in a PQQ-dependent manner, which was a PQQ-dependent enzyme found in eukaryotes. This paper presents the X-ray crystal structures of this eukaryotic PQQ-dependent quinohemoprotein, which show the active site and identifies the amino acid residues involved in binding of the cofactor PQQ. The presented X-ray structures reveal that AA12 domain is in a binary complex with the coenzyme, clearly proving that PQQ-dependent enzymes exist in eukaryotes as well as prokaryotes. Because no biosynthetic system for PQQ has been reported in eukaryotes, future research on the symbiotic systems is expected.


    Organizational Affiliation

    Department of Environmental and Natural Resource Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.,JEM Utilization Center, Japan Aerospace Exploration Agency, Tsukuba, Ibaraki, 305-8505, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.,Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan aquarius@mail.ecc.u-tokyo.ac.jp nobu1@cc.tuat.ac.jp.,Department of Biomaterial Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan aquarius@mail.ecc.u-tokyo.ac.jp nobu1@cc.tuat.ac.jp.,VTT Technical Research Centre of Finland, P.O.Box 1000, Tietotie 2, Espoo FI-02044, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular PQQ-dependent sugar dehydrogenase
A
410Coprinopsis cinereaMutation(s): 0 
Gene Names: CcSDH
Find proteins for A0A0A8IDB7 (Coprinopsis cinerea)
Go to UniProtKB:  A0A0A8IDB7
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMT
Query on FMT

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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.105 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.298α = 90.00
b = 47.851β = 115.55
c = 69.375γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHENIXphasing
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan17K17703

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release