DB code: T00233

CATH domain 3.50.50.60 : FAD/NAD(P)-binding domain Catalytic domain
3.50.50.60 : FAD/NAD(P)-binding domain Catalytic domain
3.30.390.30 : Enolase-like; domain 1
E.C. 1.11.1.1
CSA 2npx
M-CSA 2npx
MACiE

CATH domain Related DB codes (homologues)
3.50.50.60 : FAD/NAD(P)-binding domain M00163 D00015 D00041 D00042 D00045 D00064 D00071 T00004 T00015 T00017 T00025 T00211 T00213 T00242
3.30.390.30 : Enolase-like; domain 1 M00163 T00017 T00213 T00242

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P37062 NADH peroxidase
NPXase
Npx
EC 1.11.1.1
NP_814938.1 (Protein)
NC_004668.1 (DNA/RNA sequence)
PF00070 (Pyr_redox)
PF07992 (Pyr_redox_2)
PF02852 (Pyr_redox_dim)
[Graphical View]

KEGG enzyme name
NADH peroxidase
DPNH peroxidase
NAD peroxidase
diphosphopyridine nucleotide peroxidase
NADH-peroxidase
nicotinamide adenine dinucleotide peroxidase
NADH2 peroxidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P37062 NAPE_ENTFA NADH + H(2)O(2) = NAD(+) + 2 H(2)O. Homotetramer. Binds 1 FAD per subunit.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00004 C00080 C00027 C00003 C00001
E.C.
Compound FAD NADH H+ H2O2 NAD+ H2O
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotide amide group,amine group,nucleotide others others amide group,amine group,nucleotide H2O
ChEBI 16238
16908
15378
16240
15846
15377
PubChem 643975
439153
1038
22326046
784
5893
22247451
962
1f8wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1joaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1nhpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1nhqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1nhrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1nhsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1npxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
2npxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1f8wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1joaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-bound:CSO
1nhpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:CYO
1npxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Intermediate-analogue:CYO
2npxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAD Intermediate-analogue:CYO
1f8wA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1joaA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhqA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1nhsA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1npxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2npxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1joa & Swiss-prot;P37062 & literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1f8wA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10; mutant R303M
1joaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
1nhpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
1nhqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
1nhrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
1nhsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
1npxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
2npxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 10;ARG 303
1f8wA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CSX 42(O bound to CYS)
1joaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CSO 42(hydroxylation)
1nhpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant C42A
1nhqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant C42S
1nhrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 42 mutant L40C
1nhsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain OCS 42(O3 bound to CYS) mutant S41C
1npxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain OCS 42(O3 bound to CYS)
2npxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain OCS 42(O3 bound to CYS)
1f8wA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1joaA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nhpA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nhqA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nhrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nhsA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1npxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2npxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.1337-1343
[6]
Fig.6, p.225-226
[9]
p.6624-6627
[10]
[12]
Scheme 1, Scheme 2, p.2385-2386
[13]
Fig.5, p.9954-9957
[14]
[15]
p.10361-10364
[16]
p.45-46

References
[1]
Resource
Comments
Medline ID
PubMed ID 2511195
Journal J Biol Chem
Year 1989
Volume 264
Pages 19856-63
Authors Ahmed SA, Claiborne A
Title The streptococcal flavoprotein NADH oxidase. I. Evidence linking NADH oxidase and NADH peroxidase cysteinyl redox centers.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2512289
Journal J Biol Chem
Year 1989
Volume 264
Pages 21144-5
Authors Schiering N, Stoll VS, Blanchard JS, Pai EF
Title Crystallization and preliminary x-ray diffraction study of the flavoprotein NADH peroxidase from Streptococcus faecalis 10C1.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2116319
Journal FEBS Lett
Year 1990
Volume 267
Pages 186-8
Authors Stehle T, Ahmed SA, Claiborne A, Schulz GE
Title The structure of NADH peroxidase from Streptococcus faecalis at 3.3 A resolution.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS)
Medline ID 92046067
PubMed ID 1942054
Journal J Mol Biol
Year 1991
Volume 221
Pages 1325-44
Authors Stehle T, Ahmed SA, Claiborne A, Schulz GE
Title Structure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 A resolution.
Related PDB 1npx 2npx
Related UniProtKB P37062
[5]
Resource
Comments
Medline ID
PubMed ID 1740431
Journal J Biol Chem
Year 1992
Volume 267
Pages 3832-40
Authors Ahmed SA, Claiborne A
Title Active-site structural comparison of streptococcal NADH peroxidase and NADH oxidase. Reconstitution with artificial flavins.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID 93145950
PubMed ID 8425532
Journal Eur J Biochem
Year 1993
Volume 211
Pages 221-6
Authors Stehle T, Claiborne A, Schulz GE
Title NADH binding site and catalysis of NADH peroxidase.
Related PDB
Related UniProtKB P37062
[7]
Resource
Comments
Medline ID
PubMed ID 7578008
Journal Biochemistry
Year 1995
Volume 34
Pages 14114-24
Authors Crane EJ 3rd, Parsonage D, Poole LB, Claiborne A
Title Analysis of the kinetic mechanism of enterococcal NADH peroxidase reveals catalytic roles for NADH complexes with both oxidized and two-electron-reduced enzyme forms.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7766608
Journal Biochemistry
Year 1995
Volume 34
Pages 6985-92
Authors Mande SS, Parsonage D, Claiborne A, Hol WG
Title Crystallographic analyses of NADH peroxidase Cys42Ala and Cys42Ser mutants: active site structures, mechanistic implications, and an unusual environment of Arg 303.
Related PDB 1nhp 1nhq
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 7756294
Journal Biochemistry
Year 1995
Volume 34
Pages 6621-7
Authors Marcinkeviciene JA, Blanchard JS
Title Quinone reductase reaction catalyzed by Streptococcus faecalis NADH peroxidase.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7711038
Journal Biochemistry
Year 1995
Volume 34
Pages 5180-90
Authors Miller H, Mande SS, Parsonage D, Sarfaty SH, Hol WG, Claiborne A
Title An L40C mutation converts the cysteine-sulfenic acid redox center in enterococcal NADH peroxidase to a disulfide.
Related PDB 1nhr 1nhs
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 7819235
Journal Biochemistry
Year 1995
Volume 34
Pages 435-41
Authors Parsonage D, Claiborne A
Title Analysis of the kinetic and redox properties of NADH peroxidase C42S and C42A mutants lacking the cysteine-sulfenic acid redox center.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8652580
Journal Biochemistry
Year 1996
Volume 35
Pages 2380-7
Authors Crane EJ 3rd, Parsonage D, Claiborne A
Title The active-site histidine-10 of enterococcal NADH peroxidase is not essential for catalytic activity.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND ACTIVE SITE.
Medline ID 96322312
PubMed ID 8756456
Journal Biochemistry
Year 1996
Volume 35
Pages 9951-7
Authors Yeh JI, Claiborne A, Hol WG
Title Structure of the native cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 A resolution.
Related PDB 1joa
Related UniProtKB P37062
[14]
Resource
Comments STRUCTURE BY NMR
Medline ID 97361972
PubMed ID 9214307
Journal Biochemistry
Year 1997
Volume 36
Pages 8611-8
Authors Crane EJ 3rd, Vervoort J, Claiborne A
Title 13C NMR analysis of the cysteine-sulfenic acid redox center of enterococcal NADH peroxidase.
Related PDB
Related UniProtKB P37062
[15]
Resource
Comments
Medline ID
PubMed ID 10956025
Journal Biochemistry
Year 2000
Volume 39
Pages 10353-64
Authors Crane EJ 3rd, Yeh JI, Luba J, Claiborne A
Title Analysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure.
Related PDB 1f8w
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12078517
Journal Methods Enzymol
Year 2002
Volume 353
Pages 44-54
Authors Yeh JI, Claiborne A
Title Crystal structures of oxidized and reduced forms of NADH peroxidase.
Related PDB
Related UniProtKB

Comments
Although the CATH classification of the 1st domain of this enzyme is inconsistent with that of NADPH:adrenodoxin oxidoreductase (D00071 in EzCatDB), these enzymes are homologous to each other.

Created Updated
2004-03-24 2009-04-15