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Protein

NADH-cytochrome b5 reductase 3

Gene

CYB5R3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Desaturation and elongation of fatty acids, cholesterol biosynthesis, drug metabolism, and, in erythrocyte, methemoglobin reduction.

Catalytic activityi

NADH + 2 ferricytochrome b5 = NAD+ + H+ + 2 ferrocytochrome b5.

Cofactori

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi132 – 147FADBy similarityAdd BLAST16
Nucleotide bindingi171 – 206FADBy similarityAdd BLAST36

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processCholesterol biosynthesis, Cholesterol metabolism, Lipid biosynthesis, Lipid metabolism, Steroid biosynthesis, Steroid metabolism, Sterol biosynthesis, Sterol metabolism
LigandFAD, Flavoprotein, NAD

Enzyme and pathway databases

BioCyciMetaCyc:HS02015-MONOMER.
BRENDAi1.6.2.2. 2681.
ReactomeiR-HSA-196836. Vitamin C (ascorbate) metabolism.
R-HSA-211945. Phase I - Functionalization of compounds.
R-HSA-6798695. Neutrophil degranulation.
SABIO-RKiP00387.

Names & Taxonomyi

Protein namesi
Recommended name:
NADH-cytochrome b5 reductase 3 (EC:1.6.2.2)
Short name:
B5R
Short name:
Cytochrome b5 reductase
Alternative name(s):
Diaphorase-1
Cleaved into the following 2 chains:
Gene namesi
Name:CYB5R3
Synonyms:DIA1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000100243.20.
HGNCiHGNC:2873. CYB5R3.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Membrane, Mitochondrion, Mitochondrion outer membrane

Pathology & Biotechi

Involvement in diseasei

Methemoglobinemia CYB5R3-related (METHB-CYB5R3)11 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of methemoglobinemia, a hematologic disease characterized by the presence of excessive amounts of methemoglobin in blood cells, resulting in decreased oxygen carrying capacity of the blood, cyanosis and hypoxia. There are two types of methemoglobinemia CYB5R3-related. In type 1, the defect affects the soluble form of the enzyme, is restricted to red blood cells, and causes well-tolerated methemoglobinemia. In type 2, the defect affects both the soluble and microsomal forms of the enzyme and is thus generalized, affecting red cells, leukocytes and all body tissues. Type 2 methemoglobinemia is associated with mental deficiency and other neurologic symptoms.
See also OMIM:250800
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00461958R → Q in METHB-CYB5R3; type 1; 62% of activity. 3 PublicationsCorresponds to variant dbSNP:rs121965007Ensembl.1
Natural variantiVAR_01075073L → P in METHB-CYB5R3; type 1. 2 PublicationsCorresponds to variant dbSNP:rs121965013Ensembl.1
Natural variantiVAR_004620106V → M in METHB-CYB5R3; type 1; 77% of activity. 1 PublicationCorresponds to variant dbSNP:rs121965009Ensembl.1
Natural variantiVAR_004621128S → P in METHB-CYB5R3; type 2; Hiroshima. 1 PublicationCorresponds to variant dbSNP:rs121965006Ensembl.1
Natural variantiVAR_004622149L → P in METHB-CYB5R3. 1 PublicationCorresponds to variant dbSNP:rs121965008Ensembl.1
Natural variantiVAR_010752179A → V in METHB-CYB5R3; type 1. 1 PublicationCorresponds to variant dbSNP:rs201232518Ensembl.1
Natural variantiVAR_010753204C → R in METHB-CYB5R3; type 2. 1 PublicationCorresponds to variant dbSNP:rs121965011Ensembl.1
Natural variantiVAR_010754204C → Y in METHB-CYB5R3; type 1. 2 PublicationsCorresponds to variant dbSNP:rs121965015Ensembl.1
Natural variantiVAR_037315256Missing in METHB-CYB5R3; type 1; retains approximately 38% of residual diaphorase activity. 2 Publications1
Natural variantiVAR_010755273Missing in METHB-CYB5R3; type 2. 1 Publication1
Natural variantiVAR_037316292G → D in METHB-CYB5R3; type 1; retains approximately 58% of residual diaphorase activity. 2 PublicationsCorresponds to variant dbSNP:rs121965016Ensembl.1
Natural variantiVAR_004623299Missing in METHB-CYB5R3; type2; almost complete loss of activity. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi1727.
MalaCardsiCYB5R3.
MIMi250800. phenotype.
OpenTargetsiENSG00000100243.
Orphaneti139373. Recessive hereditary methemoglobinemia type 1.
139380. Recessive hereditary methemoglobinemia type 2.
PharmGKBiPA27331.

Chemistry databases

ChEMBLiCHEMBL2146.
DrugBankiDB03147. Flavin adenine dinucleotide.
DB00157. NADH.

Polymorphism and mutation databases

BioMutaiCYB5R3.
DMDMi127846.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000193922 – 301NADH-cytochrome b5 reductase 3 membrane-bound formAdd BLAST300
ChainiPRO_000001939427 – 301NADH-cytochrome b5 reductase 3 soluble formAdd BLAST275

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi2N-myristoyl glycine2 Publications1
Modified residuei42N6-acetyllysineCombined sources1
Modified residuei43PhosphotyrosineCombined sources1
Modified residuei120N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Lipoprotein, Myristate, Phosphoprotein

Proteomic databases

EPDiP00387.
MaxQBiP00387.
PaxDbiP00387.
PeptideAtlasiP00387.
PRIDEiP00387.
TopDownProteomicsiP00387-1. [P00387-1]
P00387-2. [P00387-2]

2D gel databases

REPRODUCTION-2DPAGEiIPI00446235.

PTM databases

iPTMnetiP00387.
PhosphoSitePlusiP00387.
SwissPalmiP00387.

Expressioni

Tissue specificityi

Isoform 2 is expressed at late stages of erythroid maturation.

Gene expression databases

BgeeiENSG00000100243.
CleanExiHS_CYB5R3.
ExpressionAtlasiP00387. baseline and differential.
GenevisibleiP00387. HS.

Organism-specific databases

HPAiHPA001566.

Interactioni

Subunit structurei

Component of a complex composed of cytochrome b5, NADH-cytochrome b5 reductase (CYB5R3) and MOSC2.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
HBA2P699052EBI-1046040,EBI-714680

Protein-protein interaction databases

BioGridi108071. 45 interactors.
DIPiDIP-50463N.
IntActiP00387. 12 interactors.
MINTiMINT-5003981.
STRINGi9606.ENSP00000354468.

Structurei

Secondary structure

1301
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi43 – 52Combined sources10
Beta strandi54 – 63Combined sources10
Beta strandi78 – 85Combined sources8
Beta strandi88 – 94Combined sources7
Beta strandi104 – 111Combined sources8
Beta strandi115 – 118Combined sources4
Helixi126 – 133Combined sources8
Beta strandi139 – 146Combined sources8
Beta strandi148 – 153Combined sources6
Beta strandi156 – 159Combined sources4
Beta strandi168 – 171Combined sources4
Beta strandi173 – 180Combined sources8
Helixi181 – 183Combined sources3
Helixi184 – 195Combined sources12
Beta strandi203 – 212Combined sources10
Helixi213 – 215Combined sources3
Helixi219 – 228Combined sources10
Turni230 – 232Combined sources3
Beta strandi233 – 241Combined sources9
Beta strandi247 – 252Combined sources6
Helixi255 – 261Combined sources7
Helixi265 – 267Combined sources3
Beta strandi270 – 275Combined sources6
Helixi277 – 282Combined sources6
Helixi285 – 291Combined sources7
Helixi295 – 297Combined sources3
Beta strandi298 – 300Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1M91model-A1-301[»]
1UMKX-ray1.75A27-301[»]
ProteinModelPortaliP00387.
SMRiP00387.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00387.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini40 – 152FAD-binding FR-typeAdd BLAST113

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0534. Eukaryota.
COG0543. LUCA.
GeneTreeiENSGT00390000008881.
HOGENOMiHOG000175005.
HOVERGENiHBG052580.
InParanoidiP00387.
KOiK00326.
OMAiPLHGIYI.
OrthoDBiEOG091G0EIS.
PhylomeDBiP00387.
TreeFamiTF314333.

Family and domain databases

InterProiView protein in InterPro
IPR017927. Fd_Rdtase_FAD-bd.
IPR001709. Flavoprot_Pyr_Nucl_cyt_Rdtase.
IPR001834. NADH-Cyt_B5_reductase.
IPR008333. OxRdtase_FAD-bd_dom.
IPR001433. OxRdtase_FAD/NAD-bd.
IPR017938. Riboflavin_synthase-like_b-brl.
PfamiView protein in Pfam
PF00970. FAD_binding_6. 1 hit.
PF00175. NAD_binding_1. 1 hit.
PRINTSiPR00406. CYTB5RDTASE.
PR00371. FPNCR.
SUPFAMiSSF63380. SSF63380. 1 hit.
PROSITEiView protein in PROSITE
PS51384. FAD_FR. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative promoter usage and alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P00387-1) [UniParc]FASTAAdd to basket
Also known as: M

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGAQLSTLGH MVLFPVWFLY SLLMKLFQRS TPAITLESPD IKYPLRLIDR
60 70 80 90 100
EIISHDTRRF RFALPSPQHI LGLPVGQHIY LSARIDGNLV VRPYTPISSD
110 120 130 140 150
DDKGFVDLVI KVYFKDTHPK FPAGGKMSQY LESMQIGDTI EFRGPSGLLV
160 170 180 190 200
YQGKGKFAIR PDKKSNPIIR TVKSVGMIAG GTGITPMLQV IRAIMKDPDD
210 220 230 240 250
HTVCHLLFAN QTEKDILLRP ELEELRNKHS ARFKLWYTLD RAPEAWDYGQ
260 270 280 290 300
GFVNEEMIRD HLPPPEEEPL VLMCGPPPMI QYACLPNLDH VGHPTERCFV

F
Length:301
Mass (Da):34,235
Last modified:January 23, 2007 - v3
Checksum:iFDCDCDC4EC3570B4
GO
Isoform 2 (identifier: P00387-2) [UniParc]FASTAAdd to basket
Also known as: S

The sequence of this isoform differs from the canonical sequence as follows:
     1-23: Missing.

Show »
Length:278
Mass (Da):31,629
Checksum:i229597F14FA6582E
GO
Isoform 3 (identifier: P00387-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-7: MGAQLST → MNRSLLVGCMQSKDIWGREESICERLKQDGLDVERAESWE

Note: No experimental confirmation available.
Show »
Length:334
Mass (Da):38,226
Checksum:i91CCE3D9A18621E8
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti28 – 32QRSTP → RWPRA in AAA52307 (PubMed:3035541).Curated5
Sequence conflicti29R → G in AAA59900 (PubMed:2479590).Curated1
Sequence conflicti31T → K in CAA09006 (Ref. 4) Curated1
Sequence conflicti31T → K in CAA09007 (Ref. 4) Curated1
Sequence conflicti31T → K in CAA09008 (Ref. 4) Curated1
Sequence conflicti34 – 35IT → LA in AAA52307 (PubMed:3035541).Curated2
Sequence conflicti187 – 188ML → IV in CAA09006 (Ref. 4) Curated2
Sequence conflicti187 – 188ML → IV in CAA09007 (Ref. 4) Curated2
Sequence conflicti191 – 192IR → MS in CAA09006 (Ref. 4) Curated2
Sequence conflicti191 – 192IR → MS in CAA09007 (Ref. 4) Curated2
Sequence conflicti192R → G in AAA52306 (PubMed:3035541).Curated1
Sequence conflicti233 – 234FK → CN in CAA09006 (Ref. 4) Curated2
Sequence conflicti233 – 234FK → CN in CAA09007 (Ref. 4) Curated2
Sequence conflicti280I → N in AAL87744 (Ref. 3) Curated1

Polymorphismi

Ser-117 seems to only be found in persons of African origin. The allele frequency is 0.23 in African Americans. It was not found in Caucasians, Asians, Indo-Aryans, or Arabs. There seems to be no effect on the enzyme activity.1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00461958R → Q in METHB-CYB5R3; type 1; 62% of activity. 3 PublicationsCorresponds to variant dbSNP:rs121965007Ensembl.1
Natural variantiVAR_01841966S → P3 PublicationsCorresponds to variant dbSNP:rs1130706Ensembl.1
Natural variantiVAR_01075073L → P in METHB-CYB5R3; type 1. 2 PublicationsCorresponds to variant dbSNP:rs121965013Ensembl.1
Natural variantiVAR_004620106V → M in METHB-CYB5R3; type 1; 77% of activity. 1 PublicationCorresponds to variant dbSNP:rs121965009Ensembl.1
Natural variantiVAR_010751117T → S2 PublicationsCorresponds to variant dbSNP:rs1800457Ensembl.1
Natural variantiVAR_004621128S → P in METHB-CYB5R3; type 2; Hiroshima. 1 PublicationCorresponds to variant dbSNP:rs121965006Ensembl.1
Natural variantiVAR_004622149L → P in METHB-CYB5R3. 1 PublicationCorresponds to variant dbSNP:rs121965008Ensembl.1
Natural variantiVAR_010752179A → V in METHB-CYB5R3; type 1. 1 PublicationCorresponds to variant dbSNP:rs201232518Ensembl.1
Natural variantiVAR_010753204C → R in METHB-CYB5R3; type 2. 1 PublicationCorresponds to variant dbSNP:rs121965011Ensembl.1
Natural variantiVAR_010754204C → Y in METHB-CYB5R3; type 1. 2 PublicationsCorresponds to variant dbSNP:rs121965015Ensembl.1
Natural variantiVAR_037315256Missing in METHB-CYB5R3; type 1; retains approximately 38% of residual diaphorase activity. 2 Publications1
Natural variantiVAR_010755273Missing in METHB-CYB5R3; type 2. 1 Publication1
Natural variantiVAR_037316292G → D in METHB-CYB5R3; type 1; retains approximately 58% of residual diaphorase activity. 2 PublicationsCorresponds to variant dbSNP:rs121965016Ensembl.1
Natural variantiVAR_004623299Missing in METHB-CYB5R3; type2; almost complete loss of activity. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0102001 – 23Missing in isoform 2. CuratedAdd BLAST23
Alternative sequenceiVSP_0428271 – 7MGAQLST → MNRSLLVGCMQSKDIWGREE SICERLKQDGLDVERAESWE in isoform 3. 1 Publication7

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M28713
, M28705, M28706, M28707, M28708, M28709, M28710, M28711 Genomic DNA. Translation: AAA59900.1.
Y09501 mRNA. Translation: CAA70696.1.
AF361370 mRNA. Translation: AAL87744.1.
AJ010116 mRNA. Translation: CAA09006.1.
AJ010117 mRNA. Translation: CAA09007.1.
AJ010118 mRNA. Translation: CAA09008.1.
AY341030 Genomic DNA. Translation: AAP88936.1.
BT009821 mRNA. Translation: AAP88823.1.
CR456435 mRNA. Translation: CAG30321.1.
AF061830 Genomic DNA. Translation: AAF06818.1.
AF061831 Genomic DNA. Translation: AAF06819.1.
AK302204 mRNA. Translation: BAH13649.1.
Z93241 Genomic DNA. No translation available.
BC004821 mRNA. Translation: AAH04821.1.
AJ310899 mRNA. Translation: CAC84523.1.
AJ310900 mRNA. Translation: CAC84524.1.
M16461 mRNA. Translation: AAA52306.1.
M16462 mRNA. Translation: AAA52307.1.
CCDSiCCDS14040.1. [P00387-2]
CCDS33658.1. [P00387-1]
CCDS54535.1. [P00387-3]
PIRiJS0468. RDHUB5.
RefSeqiNP_000389.1. NM_000398.6. [P00387-1]
NP_001123291.1. NM_001129819.2. [P00387-2]
NP_001165131.1. NM_001171660.1. [P00387-3]
NP_001165132.1. NM_001171661.1. [P00387-2]
NP_015565.1. NM_007326.4. [P00387-2]
UniGeneiHs.561064.

Genome annotation databases

EnsembliENST00000352397; ENSP00000338461; ENSG00000100243. [P00387-1]
ENST00000361740; ENSP00000354468; ENSG00000100243. [P00387-3]
ENST00000402438; ENSP00000385679; ENSG00000100243. [P00387-2]
ENST00000407332; ENSP00000384457; ENSG00000100243. [P00387-2]
ENST00000407623; ENSP00000384834; ENSG00000100243. [P00387-2]
GeneIDi1727.
KEGGihsa:1727.
UCSCiuc003bcx.4. human. [P00387-1]

Keywords - Coding sequence diversityi

Alternative promoter usage, Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiNB5R3_HUMAN
AccessioniPrimary (citable) accession number: P00387
Secondary accession number(s): B1AHF2
, B7Z7L3, O75675, Q8TDL8, Q8WTS8, Q9UEN4, Q9UEN5, Q9UL55, Q9UL56
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 22, 2017
This is version 228 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families