EzCatDB: S00031

DB codeS00031
CATH domainDomain 11.10.630.10Catalytic domain
E.C.1.7.1.14

CATH domainRelated DB codes (homologues)
1.10.630.10S00033,M00154,S00030

Enzyme Name
Swiss-protKEGG

P23295
Protein nameCytochrome P450 55A1nitric oxide reductase [NAD(P), nitrous oxide-forming]
fungal nitric oxide reductase
cytochrome P450nor
NOR (ambiguous)
SynonymsEC 1.14.-.-
CYPLVA1
P450 DNIR
Nitric oxide reductase
P450nor

KEGG pathways
MAP codePathways
MAP00910Nitrogen metabolism

Swiss-prot:Accession NumberP23295
Entry nameNOR_FUSOX
ActivityNitrous oxide + NAD(P)(+) + H(2)O = 2 nitric oxide + NAD(P)H.
Subunit
Subcellular location
CofactorHeme group.


CofactorsSubstratesProductsintermediates
KEGG-idC00032C00533C00004C00005C00080C00887C00003C00006C00001
CompoundHemeNitric oxideNADHNADPHH+Nitrous oxideNADNADP+H2O
Typearomatic ring (with nitrogen atoms),carboxyl group,heavy metalothersamide group,amine group,nucleotideamide group,amine group,nucleotideothersothersamide group,amine group,nucleotideamide group,amine group,nucleotideH2O
1cl6ABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-bound:HEM-_NO
1cmjABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-bound:HEM-_NO
1cmnABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-bound:HEM-_NO
1eheABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
1ehfABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
1ehgABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
1f24ABound:HEMBound:_NOUnboundUnbound
UnboundUnboundUnbound
Unbound
1f25ABound:HEMBound:_NOUnboundUnbound
UnboundUnboundUnbound
Unbound
1f26ABound:HEMBound:_NOUnboundUnbound
UnboundUnboundUnbound
Unbound
1gedABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
1geiABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-analogue:HEM-NBN
1gejABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-analogue:HEM-NBN
1jfbABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
1jfcABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-analogue:HEM-CMO
1romABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
2romABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Intermediate-analogue:HEM-CMO
1ulwABound:HEMUnboundUnboundUnbound
UnboundUnboundUnbound
Unbound
1xqdABound:HEMUnboundUnboundUnbound
UnboundAnalogue:DNDUnbound
Unbound

Active-site residues
resource
literature [8], [9], [13], [14], [15]
pdbCatalytic residuesCofactor-binding residuescomment
1cl6ATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1cmjATHR 243;       ;ASP 393
CYS 352(Heme iron binding)
mutant S286T
1cmnATHR 243;       ;ASP 393
CYS 352(Heme iron binding)
mutant S286V
1eheATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1ehfATHR 243;       ;ASP 393
CYS 352(Heme iron binding)
mutant S286T
1ehgATHR 243;       ;ASP 393
CYS 352(Heme iron binding)
mutant S286V
1f24A       ;SER 286;ASP 393
CYS 352(Heme iron binding)
mutant T243A
1f25A       ;SER 286;ASP 393
CYS 352(Heme iron binding)
mutant T243N
1f26A       ;SER 286;ASP 393
CYS 352(Heme iron binding)
mutant T243V
1gedATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1geiATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1gejATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1jfbATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1jfcATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1romATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

2romATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1ulwATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)

1xqdATHR 243;SER 286;ASP 393
CYS 352(Heme iron binding)


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.1622-1623
[5]

[7]

[9]p.830-831
[10]p.8845-8846
[11]Fig.2, p.12965
[14]p.4824-4825
[15]p.107
[16]

[22]Fig.2
[24]p.212-214

references
[1]
PubMed ID8196045
JournalJ Mol Biol
Year1994
Volume239
Pages158-9
AuthorsNakahara K, Shoun H, Adachi S, Iizuka T, Shiro Y
TitleCrystallization and preliminary X-ray diffraction studies of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum.
[2]
PubMed ID7619804
JournalBiochemistry
Year1995
Volume34
Pages9052-8
AuthorsShiro Y, Fujii M, Isogai Y, Adachi S, Iizuka T, Obayashi E, Makino R, Nakahara K, Shoun H
TitleIron-ligand structure and iron redox property of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum: relevance to its NO reduction activity.
[3]
PubMed ID7829493
JournalJ Biol Chem
Year1995
Volume270
Pages1617-23
AuthorsShiro Y, Fujii M, Iizuka T, Adachi S, Tsukamoto K, Nakahara K, Shoun H
TitleSpectroscopic and kinetic studies on reaction of cytochrome P450nor with nitric oxide. Implication for its nitric oxide reduction mechanism.
[4]
PubMed ID9010609
JournalBiochimie
Year1996
Volume78
Pages792-9
AuthorsKudo T, Tomura D, Liu DL, Dai XQ, Shoun H
TitleTwo isozymes of P450nor of Cylindrocarpon tonkinense: molecular cloning of the cDNAs and genes, expressions in the yeast, and the putative NAD(P)H-binding site.
[5]
JournalJ Biol Inorg Chem
Year1996
Volume1
Pages372-6
AuthorsRietjens IM, Osman AM, Veeger C, Zakharieva O, Antony J, Grodzicki M, Trautwein AX
TitleOn the role of the axial ligand in heme-based catalysis of the peroxidase and P450 type.
[6]
PubMed ID9003438
JournalBiochim Biophys Acta
Year1997
Volume1337
Pages66-74
AuthorsImai Y, Okamoto N, Nakahara K, Shoun H
TitleAbsorption spectral studies on heme ligand interactions of P-450nor.
[7]
PubMed ID9074619
JournalBiochim Biophys Acta
Year1997
Volume1338
Pages93-9
AuthorsToritsuka N, Shoun H, Singh UP, Park SY, Iizuka T, Shiro Y
TitleFunctional and structural comparison of nitric oxide reductases from denitrifying fungi Cylindrocarpon tonkinense and Fusarium oxysporum.
[8]
PubMed ID9256249
JournalFEBS Lett
Year1997
Volume412
Pages346-50
AuthorsPark SY, Shimizu H, Adachi S, Shiro Y, Iizuka T, Nakagawa A, Tanaka I, Shoun H, Hori H
TitleCrystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome P450nor.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
Medline ID97475224
PubMed ID9334748
JournalNat Struct Biol
Year1997
Volume4
Pages827-32
AuthorsPark SY, Shimizu H, Adachi S, Nakagawa A, Tanaka I, Nakahara K, Shoun H, Obayashi E, Nakamura H, Iizuka T, Shiro Y
TitleCrystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum.
Related PDB1rom,2rom
Related Swiss-protP23295
[10]
PubMed ID9636024
JournalBiochemistry
Year1998
Volume37
Pages8839-47
AuthorsOkamoto N, Imai Y, Shoun H, Shiro Y
TitleSite-directed mutagenesis of the conserved threonine (Thr243) of the distal helix of fungal cytochrome P450nor.
[11]
JournalJ Am Chem Soc
Year1998
Volume120
Pages12964-65
AuthorsObayashi E, Takahashi S, Shiro Y
TitleElectronic structure of reaction intermediate of cytochrome P450nor in its nitric oxide reduction.
[12]
PubMed ID10369184
JournalNitric Oxide
Year1999
Volume3
Pages142-52
AuthorsMehl M, Daiber A, Herold S, Shoun H, Ullrich V
TitlePeroxynitrite reaction with heme proteins.
[13]
PubMed ID11004439
JournalBiochim Biophys Acta
Year2000
Volume1459
Pages266-73
AuthorsHendriks J, Oubrie A, Castresana J, Urbani A, Gemeinhardt S, Saraste M
TitleNitric oxide reductases in bacteria.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS)
Medline ID20138220
PubMed ID10671516
JournalJ Biol Chem
Year2000
Volume275
Pages4816-26
AuthorsShimizu H, Obayashi E, Gomi Y, Arakawa H, Park SY, Nakamura H, Adachi S, Shoun H, Shiro Y
TitleProton delivery in NO reduction by fungal nitric-oxide reductase. Cryogenic crystallography, spectroscopy, and kinetics of ferric-NO complexes of wild-type and mutant enzymes.
Related PDB1cl6,1cmj,1cmn
Related Swiss-protP23295
[15]
CommentsX-ray crystallography
PubMed ID11132616
JournalJ Inorg Biochem
Year2000
Volume82
Pages103-11
AuthorsObayashi E, Shimizu H, Park SY, Shoun H, Shiro Y
TitleMutation effects of a conserved threonine (Thr243) of cytochrome P450nor on its structure and function.
Related PDB1f24,1f25,1f26
[16]
CommentsX-ray crystallography
PubMed ID11051564
JournalJ Inorg Biochem
Year2000
Volume81
Pages191-205
AuthorsShimizu H, Park S, Lee D, Shoun H, Shiro Y
TitleCrystal structures of cytochrome P450nor and its mutants (Ser286-->Val, Thr) in the ferric resting state at cryogenic temperature: a comparative analysis with monooxygenase cytochrome P450s.
Related PDB1ehe,1ehf,1ehg
[17]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS)
Medline ID21159060
PubMed ID11258878
JournalBiochemistry
Year2001
Volume40
Pages2669-77
AuthorsLee DS, Park SY, Yamane K, Obayashi E, Hori H, Shiro Y
TitleStructural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam.
Related PDB1gei,1gej
Related Swiss-protP23295
[18]
CommentsX-ray crystallography
PubMed ID11076941
JournalJ Biol Chem
Year2001
Volume276
Pages5020-6
AuthorsKudo T, Takaya N, Park SY, Shiro Y, Shoun H
TitleA positively charged cluster formed in the heme-distal pocket of cytochrome P450nor is essential for interaction with NADH.
Related PDB1ged
[19]
PubMed ID11346959
JournalPlanta
Year2001
Volume212
Pages835-41
AuthorsStohr C, Strube F, Marx G, Ullrich WR, Rockel P
TitleA plasma membrane-bound enzyme of tobacco roots catalyses the formation of nitric oxide from nitrite.
[20]
CommentsX-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS)
Medline ID21620774
PubMed ID11752781
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages81-9
AuthorsShimizu H, Park SY, Shiro Y, Adachi S
TitleX-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution.
Related PDB1jfb,1jfc
Related Swiss-protP23295
[21]
PubMed ID12105197
JournalJ Biol Chem
Year2002
Volume277
Pages33842-7
AuthorsZhang L, Kudo T, Takaya N, Shoun H
TitleThe B' helix determines cytochrome P450nor specificity for the electron donors NADH and NADPH.
[22]
JournalJ Mol Struct Theochem
Year2003
Volume624
Pages309-22
AuthorsTsukamoto K, Nakamura S, Shimizu K
TitleSAM1 semiempirical calculations on the catalytic cycle of nitric oxide reductase from Fusarium oxysporum.
[23]
PubMed ID14766741
JournalJ Biol Chem
Year2004
Volume279
Pages17120-5
AuthorsGronberg KL, Watmough NJ, Thomson AJ, Richardson DJ, Field SJ
TitleRedox-dependent open and closed forms of the active site of the bacterial respiratory nitric-oxide reductase revealed by cyanide binding studies.
[24]
PubMed ID15313618
JournalJ Mol Biol
Year2004
Volume342
Pages207-17
AuthorsOshima R, Fushinobu S, Su F, Zhang L, Takaya N, Shoun H
TitleStructural evidence for direct hydride transfer from NADH to cytochrome P450nor.
Related PDB1ulw,1xqd

comments
Although Swissprot data, P23295, reports that E.C. number of this enzyme is 1.14.-.-, it has been transferred to 1.7.1.14.
NAD is used as an "acceptor", whilst NADH is used as a "reduced acceptor" in this enzyme.
This enzyme catalyzes three successive reactions as follows (see [18]; These reactions are irreversible.):
(A) Fe3+ + NO -> Fe3+-NO
(B) Fe3+-NO + NADH -> Intermediate + NAD+
(C) Intermediate + NO + H+ -> Fe3+ + N2O +H2O

createdupdated
2004-05-172012-10-03
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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.