DB code: D00043

CATH domain 2.40.30.10 : Elongation Factor Tu (Ef-tu); domain 3 Catalytic domain
3.40.50.80 : Rossmann fold Catalytic domain
E.C. 1.6.2.2
CSA 1ndh
M-CSA 1ndh
MACiE

CATH domain Related DB codes (homologues)
3.40.50.80 : Rossmann fold M00006 M00141 M00159 M00164
2.40.30.10 : Elongation Factor Tu (Ef-tu); domain 3 M00006 M00141 M00159 M00164

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Contains Pfam RefSeq
P83686 NADH-cytochrome b5 reductase 3
Cytochrome b5 reductase
EC 1.6.2.2
Diaphorase-1
B5R
None PF00970 (FAD_binding_6)
PF00175 (NAD_binding_1)
[Graphical View]
P20070 NADH-cytochrome b5 reductase 3
B5R
Cytochrome b5 reductase
EC 1.6.2.2
Diaphorase-1
NADH-cytochrome b5 reductase 3 membrane-bound form
NADH-cytochrome b5 reductase 3 soluble form
PF00970 (FAD_binding_6)
PF00175 (NAD_binding_1)
[Graphical View]
NP_620232.1 (Protein)
NM_138877.1 (DNA/RNA sequence)
P00387 NADH-cytochrome b5 reductase 3
B5R
Cytochrome b5 reductase
EC 1.6.2.2
Diaphorase-1
NADH-cytochrome b5 reductase 3 membrane-bound form
NADH-cytochrome b5 reductase 3 soluble form
PF00970 (FAD_binding_6)
PF00175 (NAD_binding_1)
[Graphical View]
NP_000389.1 (Protein)
NM_000398.6 (DNA/RNA sequence)
NP_001123291.1 (Protein)
NM_001129819.2 (DNA/RNA sequence)
NP_001165131.1 (Protein)
NM_001171660.1 (DNA/RNA sequence)
NP_001165132.1 (Protein)
NM_001171661.1 (DNA/RNA sequence)
NP_015565.1 (Protein)
NM_007326.4 (DNA/RNA sequence)

KEGG enzyme name
cytochrome-b5 reductase
cytochrome b5 reductase
dihydronicotinamide adenine dinucleotide-cytochrome b5 reductase
reduced nicotinamide adeninedinucleotide-cytochrome b5 reductase
NADH-ferricytochrome b5 oxidoreductase
NADH-cytochrome b5 reductase
NADH 5alpha-reductase
NADH-cytochrome-b5 reductase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P83686 NB5R3_PIG NADH + 2 ferricytochrome b5 = NAD(+) + H(+) + 2 ferrocytochrome b5. Component of a complex composed of cytochrome b5, NADH- cytochrome b5 reductase (CYB5R3) and MOSC2. Endoplasmic reticulum membrane, Lipid- anchor, Cytoplasmic side (By similarity). Mitochondrion outer membrane, Lipid-anchor, Cytoplasmic side (By similarity). Cytoplasm (By similarity). Note=The enzyme exists in two forms, a membrane-bound form on the cytoplasmic side of the endoplasmic reticulum and also on the mitochondrial outer membrane and in soluble form in erythrocytes (By similarity). NADH-cytochrome b5 reductase 3 membrane-bound form: Endoplasmic reticulum membrane, Lipid-anchor, Cytoplasmic side (By similarity). Mitochondrion outer membrane, Lipid-anchor, Cytoplasmic side (By similarity). NADH-cytochrome b5 reductase 3 soluble form: Cytoplasm (By similarity). FAD.
P20070 NB5R3_RAT NADH + 2 ferricytochrome b5 = NAD(+) + H(+) + 2 ferrocytochrome b5. Component of a complex composed of cytochrome b5, NADH- cytochrome b5 reductase (CYB5R3) and MOSC2 (By similarity). Isoform 1: Endoplasmic reticulum membrane, Lipid-anchor, Cytoplasmic side. Mitochondrion outer membrane, Lipid-anchor, Cytoplasmic side. Isoform 3: Cytoplasm. Note=Produces the soluble form found in erythrocytes. FAD.
P00387 NB5R3_HUMAN NADH + 2 ferricytochrome b5 = NAD(+) + H(+) + 2 ferrocytochrome b5. Component of a complex composed of cytochrome b5, NADH- cytochrome b5 reductase (CYB5R3) and MOSC2 (By similarity). Isoform 1: Endoplasmic reticulum membrane, Lipid-anchor, Cytoplasmic side. Mitochondrion outer membrane, Lipid-anchor, Cytoplasmic side. Isoform 2: Cytoplasm. Note=Produces the soluble form found in erythrocytes. FAD.

KEGG Pathways
Map code Pathways E.C.
MAP00530 Aminosugars metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00004 C00996 C00080 C00003 C00999
E.C.
Compound FAD NADH Ferricytochrome b5 H+ NAD+ Ferrocytochrome b5
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotide amide group,amine group,nucleotide aromatic ring (with nitrogen atoms),carbohydrate,heavy metal others amide group,amine group,nucleotide aromatic ring (with nitrogen atoms),carbohydrate,heavy metal
ChEBI 16238
16908
15378
15846
PubChem 643975
439153
1038
5893
1ndhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1i7pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1ib0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Bound:NAD Unbound
1qx4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1qx4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1umkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound
1ndhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1i7pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ib0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qx4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qx4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1umkA02 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.
Swissprot;P83686 & literature [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ndhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 49;ARG 63;TYR 65
1i7pA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 77;ARG 91;TYR 93
1ib0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 77;ARG 91;TYR 93
1qx4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 77;ARG 91;TYR 93 mutant S127P
1qx4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 77;ARG 91;TYR 93 mutant S127P
1umkA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 77;ARG 91;TYR 93
1ndhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 272
1i7pA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 300
1ib0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 300
1qx4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 300
1qx4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 300
1umkA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 300

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[12]
p.39-40
[14]
p.299-300
[17]
[19]
Scheme II, p.3587-3588

References
[1]
Resource
Comments
Medline ID
PubMed ID 3624234
Journal J Biol Chem
Year 1987
Volume 262
Pages 11801-2
Authors Miki K, Kaida S, Kasai N, Iyanagi T, Kobayashi K, Hayashi K
Title Crystallization and preliminary x-ray crystallographic study of NADH-cytochrome b5 reductase from pig liver microsomes.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3656431
Journal J Mol Biol
Year 1987
Volume 195
Pages 749-50
Authors Takano T, Ogawa K, Sato M, Bando S, Yubisui T
Title Preliminary X-ray data of NADH-cytochrome b5 reductase from human erythrocytes.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2831990
Journal Biochim Biophys Acta
Year 1988
Volume 953
Pages 164-78
Authors Utecht RE, Kurtz DM Jr
Title Cytochrome b5 and NADH-cytochrome-b5 reductase from sipunculan erythrocytes; a methemerythrin reduction system from Phascolopsis gouldii.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2494940
Journal Arch Biochem Biophys
Year 1989
Volume 270
Pages 137-43
Authors Reif DW, Coulombe RA Jr, Aust SD
Title Vanadate-dependent NAD(P)H oxidation by microsomal enzymes.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2189408
Journal Biochem Biophys Res Commun
Year 1990
Volume 168
Pages 1285-91
Authors Hyde GE, Campbell WH
Title High-level expression in Escherichia coli of the catalytically active flavin domain of corn leaf NADH:nitrate reductase and its comparison to human NADH:cytochrome B5 reductase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2123873
Journal J Biol Chem
Year 1990
Volume 265
Pages 21709-13
Authors Strittmatter P, Hackett CS, Korza G, Ozols J
Title Characterization of the covalent cross-links of the active sites of amidinated cytochrome b5 and NADH:cytochrome b5 reductase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2019583
Journal J Biol Chem
Year 1991
Volume 266
Pages 7531-6
Authors Shirabe K, Yubisui T, Nishino T, Takeshita M
Title Role of cysteine residues in human NADH-cytochrome b5 reductase studied by site-directed mutagenesis. Cys-273 and Cys-283 are located close to the NADH-binding site but are not catalytically essential.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 1898726
Journal J Biol Chem
Year 1991
Volume 266
Pages 66-70
Authors Yubisui T, Shirabe K, Takeshita M, Kobayashi Y, Fukumaki Y, Sakaki Y, Takano T
Title Structural role of serine 127 in the NADH-binding site of human NADH-cytochrome b5 reductase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 1370824
Journal J Biol Chem
Year 1992
Volume 267
Pages 2519-23
Authors Strittmatter P, Kittler JM, Coghill JE, Ozols J
Title Characterization of lysyl residues of NADH-cytochrome b5 reductase implicated in charge-pairing with active-site carboxyl residues of cytochrome b5 by site-directed mutagenesis of an expression vector for the flavoprotein.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 7893687
Journal Biochemistry
Year 1995
Volume 34
Pages 2763-7
Authors Nishida H, Inaka K, Yamanaka M, Kaida S, Kobayashi K, Miki K
Title Crystal structure of NADH-cytochrome b5 reductase from pig liver at 2.4 A resolution.
Related PDB 1ndh
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 7890048
Journal FEBS Lett
Year 1995
Volume 361
Pages 97-100
Authors Nishida H, Inaka K, Miki K
Title Specific arrangement of three amino acid residues for flavin-binding barrel structures in NADH-cytochrome b5 reductase and the other flavin-dependent reductases.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8880927
Journal Proteins
Year 1996
Volume 26
Pages 32-41
Authors Nishida H, Miki K
Title Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: pyridine nucleotide-binding and interaction with an electron-transfer partner.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9602031
Journal Biochim Biophys Acta
Year 1998
Volume 1384
Pages 16-22
Authors Shirabe K, Nagai T, Yubisui T, Takeshita M
Title Electrostatic interaction between NADH-cytochrome b5 reductase and cytochrome b5 studied by site-directed mutagenesis.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10082957
Journal Biochim Biophys Acta
Year 1999
Volume 1430
Pages 290-301
Authors Kimura S, Emi Y, Ikushiro S, Iyanagi T
Title Systematic mutations of highly conserved His49 and carboxyl-terminal of recombinant porcine liver NADH-cytochrome b5 reductase solubilized domain.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10622712
Journal FEBS Lett
Year 1999
Volume 462
Pages 283-8
Authors Lamb DC, Kelly DE, Manning NJ, Kaderbhai MA, Kelly SL
Title Biodiversity of the P450 catalytic cycle: yeast cytochrome b5/NADH cytochrome b5 reductase complex efficiently drives the entire sterol 14-demethylation (CYP51) reaction.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11695905
Journal Biochemistry
Year 2001
Volume 40
Pages 13574-82
Authors Bewley MC, Marohnic CC, Barber MJ
Title The structure and biochemistry of NADH-dependent cytochrome b5 reductase are now consistent.
Related PDB 1i7p 1ib0
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11574067
Journal J Biochem (Tokyo)
Year 2001
Volume 130
Pages 481-90
Authors Kimura S, Nishida H, Iyanagi T
Title Effects of flavin-binding motif amino acid mutations in the NADH-cytochrome b5 reductase catalytic domain on protein stability and catalysis.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 14503867
Journal Biochemistry
Year 2003
Volume 42
Pages 11170-82
Authors Marohnic CC, Bewley MC, Barber MJ
Title Engineering and characterization of a NADPH-utilizing cytochrome b5 reductase.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12459552
Journal J Biol Chem
Year 2003
Volume 278
Pages 3580-9
Authors Kimura S, Kawamura M, Iyanagi T
Title Role of Thr(66) in porcine NADH-cytochrome b5 reductase in catalysis and control of the rate-limiting step in electron transfer.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 14609324
Journal Biochemistry
Year 2003
Volume 42
Pages 13145-51
Authors Bewley MC, Davis CA, Marohnic CC, Taormina D, Barber MJ
Title The structure of the S127P mutant of cytochrome b5 reductase that causes methemoglobinemia shows the AMP moiety of the flavin occupying the substrate binding site.
Related PDB 1qx4
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 15488472
Journal Arch Biochem Biophys
Year 2004
Volume 431
Pages 233-44
Authors Davis CA, Crowley LJ, Barber MJ
Title Cytochrome b5 reductase: the roles of the recessive congenital methemoglobinemia mutants P144L, L148P, and R159*.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 15502298
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 1929-34
Authors Bando S, Takano T, Yubisui T, Shirabe K, Takeshita M, Nakagawa A
Title Structure of human erythrocyte NADH-cytochrome b5 reductase.
Related PDB 1umk
Related UniProtKB

Comments

Created Updated
2004-12-20 2009-02-26