EzCatDB: T00233

DB codeT00233
CATH domainDomain 13.50.50.60Catalytic domain
Domain 23.50.50.60Catalytic domain
Domain 33.30.390.30
E.C.1.11.1.1
CSA2npx

CATH domainRelated DB codes (homologues)
3.30.390.30M00163,T00017,T00213,T00242
3.50.50.60M00163,D00015,D00041,D00042,D00045,D00064,D00071,T00004,T00015,T00017,T00025,T00211,T00213,T00242

Enzyme Name
Swiss-protKEGG

P37062
Protein nameNADH peroxidaseNADH peroxidase
DPNH peroxidase
NAD peroxidase
diphosphopyridine nucleotide peroxidase
NADH-peroxidase
nicotinamide adenine dinucleotide peroxidase
NADH2 peroxidase
SynonymsNPXase
Npx
EC 1.11.1.1


Swiss-prot:Accession NumberP37062
Entry nameNAPE_ENTFA
ActivityNADH + H(2)O(2) = NAD(+) + 2 H(2)O.
SubunitHomotetramer.
Subcellular location
CofactorBinds 1 FAD per subunit.


CofactorsSubstratesProductsintermediates
KEGG-idC00016C00004C00080C00027C00003C00001
CompoundFADNADHH+H2O2NAD+H2O
Typeamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotideamide group,amine group,nucleotideothersothersamide group,amine group,nucleotideH2O
1f8wA01Bound:FADUnbound
UnboundUnbound
Unbound
1joaA01Bound:FADUnbound
UnboundUnbound
Unbound
1nhpA01Bound:FADUnbound
UnboundUnbound
Unbound
1nhqA01Bound:FADUnbound
UnboundUnbound
Unbound
1nhrA01Bound:FADUnbound
UnboundUnbound
Unbound
1nhsA01Bound:FADUnbound
UnboundUnbound
Unbound
1npxA01Bound:FADUnbound
UnboundUnbound
Unbound
2npxA01Bound:FADUnbound
UnboundUnbound
Unbound
1f8wA02UnboundUnbound
UnboundUnbound
Unbound
1joaA02UnboundUnbound
UnboundUnbound
Intermediate-bound:CSO
1nhpA02UnboundUnbound
UnboundUnbound
Unbound
1nhqA02UnboundUnbound
UnboundUnbound
Unbound
1nhrA02UnboundUnbound
UnboundUnbound
Unbound
1nhsA02UnboundUnbound
UnboundUnbound
Intermediate-analogue:CYO
1npxA02UnboundUnbound
UnboundUnbound
Intermediate-analogue:CYO
2npxA02UnboundUnbound
UnboundBound:NAD
Intermediate-analogue:CYO
1f8wA03UnboundUnbound
UnboundUnbound
Unbound
1joaA03UnboundUnbound
UnboundUnbound
Unbound
1nhpA03UnboundUnbound
UnboundUnbound
Unbound
1nhqA03UnboundUnbound
UnboundUnbound
Unbound
1nhrA03UnboundUnbound
UnboundUnbound
Unbound
1nhsA03UnboundUnbound
UnboundUnbound
Unbound
1npxA03UnboundUnbound
UnboundUnbound
Unbound
2npxA03UnboundUnbound
UnboundUnbound
Unbound

Active-site residues
resource
PDB;1joa & Swiss-prot;P37062 & literature [4]
pdbCatalytic residuesModified residuescomment
1f8wA01HIS 10;       

mutant R303M
1joaA01HIS 10;ARG 303


1nhpA01HIS 10;ARG 303


1nhqA01HIS 10;ARG 303


1nhrA01HIS 10;ARG 303


1nhsA01HIS 10;ARG 303


1npxA01HIS 10;ARG 303


2npxA01HIS 10;ARG 303


1f8wA02      
CSX 42(O bound to CYS) 

1joaA02      
CSO 42(hydroxylation)  

1nhpA02      
                       
mutant C42A
1nhqA02      
                       
mutant C42S
1nhrA02CYS 42
                       
mutant L40C
1nhsA02      
OCS 42(O3 bound to CYS)
mutant S41C
1npxA02      
OCS 42(O3 bound to CYS)

2npxA02      
OCS 42(O3 bound to CYS)

1f8wA03


1joaA03


1nhpA03


1nhqA03


1nhrA03


1nhsA03


1npxA03


2npxA03



References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID2511195
JournalJ Biol Chem
Year1989
Volume264
Pages19856-63
AuthorsAhmed SA, Claiborne A
TitleThe streptococcal flavoprotein NADH oxidase. I. Evidence linking NADH oxidase and NADH peroxidase cysteinyl redox centers.
[2]
PubMed ID2512289
JournalJ Biol Chem
Year1989
Volume264
Pages21144-5
AuthorsSchiering N, Stoll VS, Blanchard JS, Pai EF
TitleCrystallization and preliminary x-ray diffraction study of the flavoprotein NADH peroxidase from Streptococcus faecalis 10C1.
[3]
PubMed ID2116319
JournalFEBS Lett
Year1990
Volume267
Pages186-8
AuthorsStehle T, Ahmed SA, Claiborne A, Schulz GE
TitleThe structure of NADH peroxidase from Streptococcus faecalis at 3.3 A resolution.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS)
Medline ID92046067
PubMed ID1942054
JournalJ Mol Biol
Year1991
Volume221
Pages1325-44
AuthorsStehle T, Ahmed SA, Claiborne A, Schulz GE
TitleStructure of NADH peroxidase from Streptococcus faecalis 10C1 refined at 2.16 A resolution.
Related PDB1npx,2npx
Related Swiss-protP37062
[5]
PubMed ID1740431
JournalJ Biol Chem
Year1992
Volume267
Pages3832-40
AuthorsAhmed SA, Claiborne A
TitleActive-site structural comparison of streptococcal NADH peroxidase and NADH oxidase. Reconstitution with artificial flavins.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID93145950
PubMed ID8425532
JournalEur J Biochem
Year1993
Volume211
Pages221-6
AuthorsStehle T, Claiborne A, Schulz GE
TitleNADH binding site and catalysis of NADH peroxidase.
Related Swiss-protP37062
[7]
PubMed ID7578008
JournalBiochemistry
Year1995
Volume34
Pages14114-24
AuthorsCrane EJ 3rd, Parsonage D, Poole LB, Claiborne A
TitleAnalysis of the kinetic mechanism of enterococcal NADH peroxidase reveals catalytic roles for NADH complexes with both oxidized and two-electron-reduced enzyme forms.
[8]
CommentsX-ray crystallography
PubMed ID7766608
JournalBiochemistry
Year1995
Volume34
Pages6985-92
AuthorsMande SS, Parsonage D, Claiborne A, Hol WG
TitleCrystallographic analyses of NADH peroxidase Cys42Ala and Cys42Ser mutants: active site structures, mechanistic implications, and an unusual environment of Arg 303.
Related PDB1nhp,1nhq
[9]
PubMed ID7756294
JournalBiochemistry
Year1995
Volume34
Pages6621-7
AuthorsMarcinkeviciene JA, Blanchard JS
TitleQuinone reductase reaction catalyzed by Streptococcus faecalis NADH peroxidase.
[10]
CommentsX-ray crystallography
PubMed ID7711038
JournalBiochemistry
Year1995
Volume34
Pages5180-90
AuthorsMiller H, Mande SS, Parsonage D, Sarfaty SH, Hol WG, Claiborne A
TitleAn L40C mutation converts the cysteine-sulfenic acid redox center in enterococcal NADH peroxidase to a disulfide.
Related PDB1nhr,1nhs
[11]
PubMed ID7819235
JournalBiochemistry
Year1995
Volume34
Pages435-41
AuthorsParsonage D, Claiborne A
TitleAnalysis of the kinetic and redox properties of NADH peroxidase C42S and C42A mutants lacking the cysteine-sulfenic acid redox center.
[12]
PubMed ID8652580
JournalBiochemistry
Year1996
Volume35
Pages2380-7
AuthorsCrane EJ 3rd, Parsonage D, Claiborne A
TitleThe active-site histidine-10 of enterococcal NADH peroxidase is not essential for catalytic activity.
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND ACTIVE SITE.
Medline ID96322312
PubMed ID8756456
JournalBiochemistry
Year1996
Volume35
Pages9951-7
AuthorsYeh JI, Claiborne A, Hol WG
TitleStructure of the native cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 A resolution.
Related PDB1joa
Related Swiss-protP37062
[14]
CommentsSTRUCTURE BY NMR
Medline ID97361972
PubMed ID9214307
JournalBiochemistry
Year1997
Volume36
Pages8611-8
AuthorsCrane EJ 3rd, Vervoort J, Claiborne A
Title13C NMR analysis of the cysteine-sulfenic acid redox center of enterococcal NADH peroxidase.
Related Swiss-protP37062
[15]
PubMed ID10956025
JournalBiochemistry
Year2000
Volume39
Pages10353-64
AuthorsCrane EJ 3rd, Yeh JI, Luba J, Claiborne A
TitleAnalysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure.
Related PDB1f8w
[16]
PubMed ID12078517
JournalMethods Enzymol
Year2002
Volume353
Pages44-54
AuthorsYeh JI, Claiborne A
TitleCrystal structures of oxidized and reduced forms of NADH peroxidase.

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.

createdupdated
2004-03-242009-04-15
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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