DB code: S00219

CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 1.6.99.1
CSA 1oya
M-CSA 1oya
MACiE M0319

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 S00217 S00218 S00532 S00198 S00220 S00745 S00537 S00538 S00539 S00826 S00841 S00235 S00239 S00240 S00243 S00244 S00199 S00200 S00201 S00221 S00222 S00847 S00224 S00225 S00226 D00014 D00029 M00141 T00015 T00239 D00664 D00665 D00804 D00863 T00089

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
Q02899 NADPH dehydrogenase 1
EC 1.6.99.1
Old yellow enzyme 1
PF00724 (Oxidored_FMN)
[Graphical View]

KEGG enzyme name
NADPH dehydrogenase
NADPH2 diaphorase
NADPH diaphorase
OYE
diaphorase
dihydronicotinamide adenine dinucleotide phosphate dehydrogenase
NADPH-dehydrogenase
NADPH-diaphorase
NADPH2-dehydrogenase
old yellow enzyme
reduced nicotinamide adenine dinucleotide phosphate dehydrogenase
TPNH dehydrogenase
TPNH-diaphorase
triphosphopyridine diaphorase
triphosphopyridine nucleotide diaphorase
NADPH2 dehydrogenase
NADPH:(acceptor) oxidoreductase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q02899 OYE1_SACPS NADPH + acceptor = NADP(+) + reduced acceptor. Homodimer or heterodimer. FMN.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00061 C00005 C02395 C00007 C00080 C00006 C00414 C00027
E.C.
Compound FMN NADPH Cyclohex-2-enone O2 H+ NADP+ Cyclohexanone H2O2
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,phosphate group/phosphate ion amide group,amine group,nucleotide carbohydrate others others amide group,amine group,nucleotide carbohydrate others
ChEBI 17621
16474
15977
27140
26689
15379
15378
18009
17854
16240
PubChem 643976
5884
13594
977
1038
5886
7967
784
22326046
1bwkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1bwlA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1k02A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1k03A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Analogue:HBA Unbound Unbound Unbound Unbound
1oyaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound
1oybA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Analogue:HBA Unbound Unbound Unbound Unbound
1oycA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FMN Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1bwk, 1bwl & literature;[3], [5], [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bwkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASN 194;TYR 196 mutant H191N
1bwlA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; ;TYR 196 mutant H191N;N194N
1k02A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 191;ASN 194;TYR 196 mutant Q114N
1k03A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 191;ASN 194;TYR 196 mutant Q114N
1oyaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 191;ASN 194;TYR 196
1oybA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 191;ASN 194;TYR 196
1oycA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 191;ASN 194;TYR 196

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Scheme I 6
[4]
p.1523-1525 1
[5]
[6]
Fig.1, Fig.7, p.32768-32770 5
[7]
Fig.2
[8]
p.3561
[9]
Scheme 11, Scheme 12, p.294-295
[10]
Scheme 1, Scheme 3, p.10738
[11]
Fig.1, Fig.4
[12]
Scheme 1
[14]
Fig.5, p.2144 3
[17]
p.1609-1612

References
[1]
Resource
Comments
Medline ID
PubMed ID 3091069
Journal Biochemistry
Year 1986
Volume 25
Pages 4077-84
Authors Peterson DM, Fisher J
Title Autocatalytic quinone methide formation from mitomycin c.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8230231
Journal J Mol Biol
Year 1993
Volume 234
Pages 502-7
Authors Fox KM, Karplus PA
Title Crystallization of Old Yellow Enzyme illustrates an effective strategy for increasing protein crystal size.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID 95187711
PubMed ID 7881908
Journal Structure
Year 1994
Volume 2
Pages 1089-105
Authors Fox KM, Karplus PA
Title Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins.
Related PDB 1oya 1oyb 1oyc
Related UniProtKB Q02899
[4]
Resource
Comments
Medline ID
PubMed ID 8529830
Journal FASEB J
Year 1995
Volume 9
Pages 1518-26
Authors Karplus PA, Fox KM, Massey V
Title Flavoprotein structure and mechanism. 8. Structure-function relations for old yellow enzyme.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9830019
Journal J Biol Chem
Year 1998
Volume 273
Pages 32753-62
Authors Brown BJ, Deng Z, Karplus PA, Massey V
Title On the active site of Old Yellow Enzyme. Role of histidine 191 and asparagine 194.
Related PDB 1bwk 1bwl
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9830020
Journal J Biol Chem
Year 1998
Volume 273
Pages 32763-70
Authors Kohli RM, Massey V
Title The oxidative half-reaction of Old Yellow Enzyme. The role of tyrosine 196.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 10092614
Journal J Biol Chem
Year 1999
Volume 274
Pages 9357-62
Authors Fox KM, Karplus PA
Title The flavin environment in old yellow enzyme. An evaluation of insights from spectroscopic and artificial flavin studies.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10097075
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 3556-61
Authors Xu D, Kohli RM, Massey V
Title The role of threonine 37 in flavin reactivity of the old yellow enzyme.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10961912
Journal Biochem Soc Trans
Year 2000
Volume 28
Pages 283-96
Authors Massey V
Title The chemical and biological versatility of riboflavin.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10995477
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 10733-8
Authors Meah Y, Massey V
Title Old yellow enzyme: stepwise reduction of nitro-olefins and catalysis of aci-nitro tautomerization.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10694883
Journal Trends Biochem Sci
Year 2000
Volume 25
Pages 126-32
Authors Fraaije MW, Mattevi A
Title Flavoenzymes: diverse catalysts with recurrent features.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11438708
Journal Proc Natl Acad Sci U S A
Year 2001
Volume 98
Pages 8560-5
Authors Meah Y, Brown BJ, Chakraborty S, Massey V
Title Old yellow enzyme: reduction of nitrate esters, glycerin trinitrate, and propylene 1,2-dinitrate.
Related PDB
Related UniProtKB
[13]
Resource
Comments Homologous enzyme
Medline ID
PubMed ID 11377202
Journal Structure (Camb)
Year 2001
Volume 9
Pages 419-29
Authors Breithaupt C, Strassner J, Breitinger U, Huber R, Macheroux P, Schaller A, Clausen T
Title X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11668181
Journal J Biol Chem
Year 2002
Volume 277
Pages 2138-45
Authors Brown BJ, Hyun JW, Duvvuri S, Karplus PA, Massey V
Title The role of glutamine 114 in old yellow enzyme.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12186866
Journal J Biol Chem
Year 2002
Volume 277
Pages 41507-16
Authors Chakraborty S, Massey V
Title Reaction of reduced flavins and flavoproteins with diphenyliodonium chloride.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12417633
Journal J Exp Med
Year 2002
Volume 196
Pages 1241-51
Authors Kubata BK, Kabututu Z, Nozaki T, Munday CJ, Fukuzumi S, Ohkubo K, Lazarus M, Maruyama T, Martin SK, Duszenko M, Urade Y
Title A key role for old yellow enzyme in the metabolism of drugs by Trypanosoma cruzi.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 12055282
Journal Microbiology
Year 2002
Volume 148
Pages 1607-14
Authors Williams RE, Bruce NC
Title New uses for an Old Enzyme'--the Old Yellow Enzyme family of flavoenzymes.
Related PDB
Related UniProtKB

Comments
This enzyme catalyzes two separate reactions, reductive half-reaction and oxidative half-reaction. In the reductive half-reaction, NADPH is reduced to be NADP+. In the oxidative half-reaction, O2 or alpha,beta-unsaturated ketone/aldehyde is oxidized to be H2O2 or reduced ketone/aldehyde, respectively (see [6]).
Reductive half-reaction:
(A) Hydride transfer from NADPH to FMN, giving NADP+ and FMNH2:
Oxidative half-reaction:
(B) Hydride transfer from FMNH2 to unsaturated ketone/aldehyde, giving FMN and reduced ketone/aldehyde:
or
(C) Hydride transfer from FMNH2 to O2, giving FMN and H2O2:

Created Updated
2004-08-04 2009-02-26