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Protein

Pyranose dehydrogenase 1

Gene

pdh1

Organism
Leucoagaricus meleagris (Western flat-topped agaric) (Agaricus meleagris)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the single-oxidation or sequential double oxidation reaction of carbohydrates primarily at carbon-2 and/or carbon-3 with the concomitant reduction of the flavin. The enzyme exhibits a broad sugar substrate specificity, oxidizing different aldopyranoses to the corresponding C-1, C-2, C-3 or C-1,2, C-2,3 and C-3,4 (di)dehydro sugars with substrate-specific regioselectivity. Accepts only a narrow range of electron acceptors such as substituted benzoquinones and complexed metal ions and reacts extremely slowly with O2 as acceptor. May play a role in the natural recycling of plant matter by oxidizing all major monosaccharides in lignocellulose and by reducing quinone compounds or reactive radical species generated during lignin depolymerization.3 Publications

Catalytic activityi

Pyranose + acceptor = pyranos-2-ulose + reduced acceptor.3 Publications
Pyranose + acceptor = pyranos-3-ulose + reduced acceptor.3 Publications
Pyranose + acceptor = pyranos-2,3-diulose + reduced acceptor.3 Publications
A pyranoside + acceptor = a pyranosid-3-ulose + reduced acceptor.3 Publications
A pyranoside + acceptor = a pyranosid-3,4-diulose + reduced acceptor.3 Publications

Cofactori

FAD2 PublicationsNote: Binds 1 FAD covalently per subunit.2 Publications

Kineticsi

  1. KM=0.82 mM for D-glucose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  2. KM=6.82 mM for cellobiose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  3. KM=8.61 mM for D-maltose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  4. KM=156 mM for maltotriose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  5. KM=108 mM for D-mannose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  6. KM=1.05 mM for D-galactose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  7. KM=137 mM for L-sorbose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  8. KM=59.7 mM for D-ribose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  9. KM=79.1 mM for D-talose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  10. KM=1.93 mM for D-xylose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  11. KM=0.54 mM for L-arabinose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  12. KM=10.8 mM for xylobiose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  13. KM=153 mM for D-fructose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  14. KM=134 mM for lactose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  15. KM=0.13 mM for ferricenium (at pH 8.5 with D-glucose as substrate)1 Publication
  16. KM=1.82 mM for 1,4-benzoquinone (at pH 3.0 with D-glucose as substrate)1 Publication
  17. KM=0.55 mM for 2-chloro-1,4-benzoquinone (at pH 5.0 with D-glucose as substrate)1 Publication
  18. KM=0.92 mM for 2,5-dichloro-1,4-benzoquinone (at pH 5.0 with D-glucose as substrate)1 Publication
  19. KM=0.18 mM for methyl-1,4-benzoquinone (at pH 8.0 with D-glucose as substrate)1 Publication
  20. KM=0.22 mM for 3,5-di-tert-butyl-benzoquinone (at pH 6.0 with D-glucose as substrate)1 Publication
  21. KM=0.14 mM for 2,6-dichloroindophenol (at pH 4.0 with D-glucose as substrate)1 Publication
  1. Vmax=41.4 µmol/min/mg enzyme for D-glucose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  2. Vmax=34.5 µmol/min/mg enzyme for cellobiose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  3. Vmax=38.9 µmol/min/mg enzyme for D-maltose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  4. Vmax=21.3 µmol/min/mg enzyme for maltotriose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  5. Vmax=26.4 µmol/min/mg enzyme for D-mannose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  6. Vmax=43.7 µmol/min/mg enzyme for D-galactose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  7. Vmax=14.1 µmol/min/mg enzyme for L-sorbose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  8. Vmax=28.2 µmol/min/mg enzyme for D-ribose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  9. Vmax=19.2 µmol/min/mg enzyme for D-talose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  10. Vmax=39.1 µmol/min/mg enzyme for D-xylose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  11. Vmax=33.5 µmol/min/mg enzyme for L-arabinose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  12. Vmax=45.4 µmol/min/mg enzyme for xylobiose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  13. Vmax=14.9 µmol/min/mg enzyme for D-fructose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  14. Vmax=35.6 µmol/min/mg enzyme for lactose (with ferricenium ion (Fc+) as electron acceptor)1 Publication
  15. Vmax=93.9 µmol/min/mg enzyme for ferricenium (at pH 8.5 with D-glucose as substrate)1 Publication
  16. Vmax=68.5 µmol/min/mg enzyme for 1,4-benzoquinone (at pH 3.0 with D-glucose as substrate)1 Publication
  17. Vmax=13.6 µmol/min/mg enzyme for 2-chloro-1,4-benzoquinone (at pH 5.0 with D-glucose as substrate)1 Publication
  18. Vmax=2.78 µmol/min/mg enzyme for 2,5-dichloro-1,4-benzoquinone (at pH 5.0 with D-glucose as substrate)1 Publication
  19. Vmax=2.7 µmol/min/mg enzyme for methyl-1,4-benzoquinone (at pH 8.0 with D-glucose as substrate)1 Publication
  20. Vmax=95.6 µmol/min/mg enzyme for 3,5-di-tert-butyl-benzoquinone (at pH 6.0 with D-glucose as substrate)1 Publication
  21. Vmax=56.3 µmol/min/mg enzyme for 2,6-dichloroindophenol (at pH 4.0 with D-glucose as substrate)1 Publication

pH dependencei

Optimum pH is 9 with ferricenium ion (Fc+) as electron acceptor. The enzyme is stable from pH 4 to pH 10.1 Publication

Temperature dependencei

Optimum temperature is 63 degrees Celsius with ferricenium ion (Fc+) as electron acceptor.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei537 – 5371Proton acceptor1 Publication
Active sitei581 – 58111 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

FAD, Flavoprotein

Enzyme and pathway databases

BRENDAi1.1.99.29. 7355.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyranose dehydrogenase 11 Publication (EC:1.1.99.293 Publications)
Short name:
PDH 11 Publication
Alternative name(s):
Pyranose:quinone oxidoreductase 11 Publication
Gene namesi
Name:pdh11 Publication
OrganismiLeucoagaricus meleagris (Western flat-topped agaric) (Agaricus meleagris)
Taxonomic identifieri201219 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaAgaricomycotinaAgaricomycetesAgaricomycetidaeAgaricalesAgaricaceaeLeucoagaricus

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 25251 PublicationAdd
BLAST
Chaini26 – 602577Pyranose dehydrogenase 1PRO_0000431287Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi100 – 1001N-linked (GlcNAc...)1 Publication
Modified residuei128 – 1281Tele-8alpha-FAD histidine1 Publication
Glycosylationi200 – 2001N-linked (GlcNAc...)PROSITE-ProRule annotation
Glycosylationi277 – 2771N-linked (GlcNAc...)PROSITE-ProRule annotation
Glycosylationi344 – 3441N-linked (GlcNAc...)1 Publication

Post-translational modificationi

N-glycosylated.1 Publication

Keywords - PTMi

Glycoprotein

Expressioni

Inductioni

Induced by carbon starvation.1 Publication

Interactioni

Subunit structurei

Monomer.1 Publication

Structurei

Secondary structure

1
602
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 315Combined sources
Helixi32 – 343Combined sources
Beta strandi42 – 465Combined sources
Helixi50 – 5910Combined sources
Beta strandi67 – 704Combined sources
Helixi80 – 834Combined sources
Helixi85 – 906Combined sources
Turni107 – 1115Combined sources
Helixi124 – 1274Combined sources
Helixi138 – 14811Combined sources
Helixi151 – 1533Combined sources
Helixi155 – 16511Combined sources
Beta strandi166 – 1683Combined sources
Helixi183 – 1853Combined sources
Beta strandi188 – 1958Combined sources
Helixi202 – 21312Combined sources
Turni215 – 2173Combined sources
Beta strandi231 – 2344Combined sources
Beta strandi237 – 2393Combined sources
Helixi248 – 2514Combined sources
Turni252 – 2554Combined sources
Beta strandi260 – 2634Combined sources
Beta strandi267 – 2726Combined sources
Beta strandi274 – 2807Combined sources
Beta strandi283 – 2897Combined sources
Beta strandi295 – 2984Combined sources
Beta strandi300 – 3056Combined sources
Helixi308 – 31811Combined sources
Helixi324 – 3296Combined sources
Beta strandi335 – 3373Combined sources
Turni339 – 3424Combined sources
Beta strandi343 – 3464Combined sources
Beta strandi349 – 3579Combined sources
Helixi366 – 37611Combined sources
Helixi380 – 3823Combined sources
Beta strandi389 – 3935Combined sources
Helixi397 – 3993Combined sources
Beta strandi401 – 4033Combined sources
Beta strandi406 – 4083Combined sources
Beta strandi413 – 42412Combined sources
Helixi439 – 4413Combined sources
Beta strandi443 – 45311Combined sources
Beta strandi459 – 4624Combined sources
Beta strandi464 – 4663Combined sources
Beta strandi473 – 4753Combined sources
Helixi482 – 49918Combined sources
Helixi502 – 5043Combined sources
Turni505 – 5073Combined sources
Beta strandi508 – 5136Combined sources
Turni514 – 5174Combined sources
Helixi521 – 53111Combined sources
Beta strandi558 – 5603Combined sources
Beta strandi564 – 5685Combined sources
Helixi571 – 5733Combined sources
Beta strandi574 – 5763Combined sources
Helixi583 – 60018Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H7UX-ray1.60A1-602[»]
ProteinModelPortaliQ3L245.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GMC oxidoreductase family.Curated

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.50.50.60. 3 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR012132. GMC_OxRdtase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000137. Alcohol_oxidase. 1 hit.
SUPFAMiSSF51905. SSF51905. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q3L245-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLPRVTKLNS RLLSLALLGI QIARGAITYQ HPDDLPSGVD YDFIVAGGGT
60 70 80 90 100
AGLVVASRLS ENSNWKVLVI EAGPSNKDAF VTRVPGLAST LGAGSPIDWN
110 120 130 140 150
YTTIPQDGLD GRSLDYPRAK ILGGCSTHNG MVYTRGSKDD WNSWAGIIGD
160 170 180 190 200
QGLGWDSILP AIKKAEKFTQ DFTDQSVKGH IDPSVHGFDG KLSVSAAYSN
210 220 230 240 250
ISFNDLLFET TKELNAEFPF KLDMNDGKPI GLGWTQYTID NHAERSSSAT
260 270 280 290 300
SYLESTGDNV HVLVNTLVTR VLSASGNGTD FRKVEFAVDA NSPKKQLEAK
310 320 330 340 350
KEVIVAGGVI ASPQILMNSG IGERKVLQAV GIDTLIDNPS VGKNLSDQGA
360 370 380 390 400
TSVMFDTTLP STDFDVDAAL TEWTNSHTGP LARGARLNHL TFVRLPDDKL
410 420 430 440 450
NGQDPSSGKN SPHIEFQFAQ ITPQVPTLGV PKQAPLPAAN SYRLLLQLAV
460 470 480 490 500
VNLYSISRGS ISLSDNNPFT YPLIDLNMFK EDIDIAILRE GIRSAGRMFS
510 520 530 540 550
SKAFKNSVNK FVYPPADATS DEDLDAFLRS STFSYVHGVG TLSMSPKGAS
560 570 580 590 600
WGVVNPDFKV KGTSGLRVVD ASVIPHAPAA HTQLPVYAFA EYASALIAKS

YN
Length:602
Mass (Da):64,684
Last modified:November 8, 2005 - v1
Checksum:iEC7A73CABCA75DBE
GO

Mass spectrometryi

Molecular mass is 66547 Da from positions 26 - 602. Determined by MALDI. Mass of the N-glycosylated protein.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY753306 Genomic DNA. Translation: AAW82996.1.
AY753307 mRNA. Translation: AAW82997.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY753306 Genomic DNA. Translation: AAW82996.1.
AY753307 mRNA. Translation: AAW82997.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H7UX-ray1.60A1-602[»]
ProteinModelPortaliQ3L245.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi1.1.99.29. 7355.

Family and domain databases

Gene3Di3.50.50.60. 3 hits.
InterProiIPR023753. FAD/NAD-binding_dom.
IPR012132. GMC_OxRdtase.
IPR000172. GMC_OxRdtase_N.
IPR007867. GMC_OxRtase_C.
[Graphical view]
PfamiPF05199. GMC_oxred_C. 1 hit.
PF00732. GMC_oxred_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000137. Alcohol_oxidase. 1 hit.
SUPFAMiSSF51905. SSF51905. 2 hits.
ProtoNetiSearch...

Publicationsi

  1. "Molecular cloning of three pyranose dehydrogenase-encoding genes from Agaricus meleagris and analysis of their expression by real-time RT-PCR."
    Kittl R., Sygmund C., Halada P., Volc J., Divne C., Haltrich D., Peterbauer C.K.
    Curr. Genet. 53:117-127(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], INDUCTION.
    Strain: CCBAS 907.
  2. "Characterization of pyranose dehydrogenase from Agaricus meleagris and its application in the C-2 specific conversion of D-galactose."
    Sygmund C., Kittl R., Volc J., Halada P., Kubatova E., Haltrich D., Peterbauer C.K.
    J. Biotechnol. 133:334-342(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 26-35, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, SUBUNIT, GLYCOSYLATION, MASS SPECTROMETRY.
    Strain: CCBAS 907.
  3. "A new enzyme catalysis: 3,4-dioxidation of some aryl beta-D-glycopyranosides by fungal pyranose dehydrogenase."
    Sedmera P., Halada P., Peterbauer C., Volc J.
    Tetrahedron Lett. 45:8677-8680(2004)
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
    Strain: CCBAS 907.
  4. "New biotransformations of some reducing sugars to the corresponding (di)dehydro(glycosyl) aldoses or aldonic acids using fungal pyranose dehydrogenase."
    Sedmera P., Halada P., Kubatova E., Haltrich D., Prikrylova V., Volc J.
    J. Mol. Catal., B Enzym. 41:32-42(2006)
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
    Strain: CCBAS 907.
  5. "The 1.6 A crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate."
    Tan T.C., Spadiut O., Wongnate T., Sucharitakul J., Krondorfer I., Sygmund C., Haltrich D., Chaiyen P., Peterbauer C.K., Divne C.
    PLoS ONE 8:E53567-E53567(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH FAD, GLYCOSYLATION AT ASN-100 AND ASN-344, COFACTOR, ACTIVE SITE.

Entry informationi

Entry nameiPDH1_LEUMG
AccessioniPrimary (citable) accession number: Q3L245
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 26, 2014
Last sequence update: November 8, 2005
Last modified: December 9, 2015
This is version 48 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.