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O43837 (IDH3B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 149. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial

EC=1.1.1.41
Alternative name(s):
Isocitric dehydrogenase subunit beta
NAD(+)-specific ICDH subunit beta
Gene names
Name:IDH3B
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length385 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH.

Cofactor

Binds 1 magnesium or manganese ion per subunit By similarity.

Subunit structure

Heterooligomer of subunits alpha, beta, and gamma in the apparent ratio of 2:1:1 By similarity.

Subcellular location

Mitochondrion.

Involvement in disease

Retinitis pigmentosa 46 (RP46) [MIM:612572]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9

Sequence similarities

Belongs to the isocitrate and isopropylmalate dehydrogenases family.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform B (identifier: O43837-1)

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.
Isoform A (identifier: O43837-2)

The sequence of this isoform differs from the canonical sequence as follows:
     361-385: RDMGGYSTTTDFIKSVIGHLQTKGS → SDMGGYATCHDFTEAVIAALPHP
Isoform C (identifier: O43837-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-177: MAALSGVRWL...EGEYSSLEHE → MKMGERWSSLFPFPVSPSCCFLLTQ

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 3434Mitochondrion By similarity
Chain35 – 385351Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial
PRO_0000014444

Sites

Metal binding2511Magnesium or manganese By similarity
Binding site1331Substrate By similarity
Binding site1641Substrate By similarity
Binding site2511Substrate By similarity
Site1711Critical for catalysis By similarity
Site2181Critical for catalysis By similarity

Amino acid modifications

Modified residue1991N6-acetyllysine Ref.7

Natural variations

Alternative sequence1 – 177177MAALS…SLEHE → MKMGERWSSLFPFPVSPSCC FLLTQ in isoform C.
VSP_041335
Alternative sequence361 – 38525RDMGG…QTKGS → SDMGGYATCHDFTEAVIAAL PHP in isoform A.
VSP_002462
Natural variant31A → V. Ref.1
Corresponds to variant rs3178817 [ dbSNP | Ensembl ].
VAR_022660
Natural variant1321L → P in RP46. Ref.9
VAR_054851
Natural variant1661Q → H.
Corresponds to variant rs11542741 [ dbSNP | Ensembl ].
VAR_049781
Natural variant3601T → A.
Corresponds to variant rs8296 [ dbSNP | Ensembl ].
VAR_056005

Experimental info

Sequence conflict127 – 1304SYDM → RTLV in CAB43266. Ref.6
Sequence conflict2501I → V in BAA91971. Ref.2
Sequence conflict3851S → SNL in AAD09340. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform B [UniParc].

Last modified May 1, 2007. Version 2.
Checksum: 7324E6CC30A68EE2

FASTA38542,184
        10         20         30         40         50         60 
MAALSGVRWL TRALVSAGNP GAWRGLSTSA AAHAASRSQA EDVRVEGSFP VTMLPGDGVG 

        70         80         90        100        110        120 
PELMHAVKEV FKAAAVPVEF QEHHLSEVQN MASEEKLEQV LSSMKENKVA IIGKIHTPME 

       130        140        150        160        170        180 
YKGELASYDM RLRRKLDLFA NVVHVKSLPG YMTRHNNLDL VIIREQTEGE YSSLEHESAR 

       190        200        210        220        230        240 
GVIECLKIVT RAKSQRIAKF AFDYATKKGR GKVTAVHKAN IMKLGDGLFL QCCEEVAELY 

       250        260        270        280        290        300 
PKIKFETMII DNCCMQLVQN PYQFDVLVMP NLYGNIIDNL AAGLVGGAGV VPGESYSAEY 

       310        320        330        340        350        360 
AVFETGARHP FAQAVGRNIA NPTAMLLSAS NMLRHLNLEY HSSMIADAVK KVIKVGKVRT 

       370        380 
RDMGGYSTTT DFIKSVIGHL QTKGS 

« Hide

Isoform A [UniParc].

Checksum: 6B5A3D3F82CCDB34
Show »

FASTA38341,887
Isoform C [UniParc].

Checksum: 7036C0A641A17E2D
Show »

FASTA23325,555

References

« Hide 'large scale' references
[1]"Identification and functional characterization of a novel, tissue-specific NAD+-dependent isocitrate dehydrogenase beta subunit isoform."
Kim Y.-O., Koh H.-J., Kim S.-H., Jo S.-H., Huh J.-W., Jeong K.-S., Lee I.J., Song B.J., Huh T.-L.
J. Biol. Chem. 274:36866-36875(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND B), VARIANT VAL-3, ALTERNATIVE SPLICING.
Tissue: Heart.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS B AND C).
Tissue: Placenta and Synovium.
[3]"The DNA sequence and comparative analysis of human chromosome 20."
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. expand/collapse author list , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM B).
Tissue: Lung.
[6]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 127-385 (ISOFORM B).
Tissue: Uterus.
[7]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-199, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle."
Hartong D.T., Dange M., McGee T.L., Berson E.L., Dryja T.P., Colman R.F.
Nat. Genet. 40:1230-1234(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT RP46 PRO-132.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U49283 mRNA. Translation: AAB94295.1.
AF023265 mRNA. Translation: AAD09339.1.
AF023266 mRNA. Translation: AAD09340.1.
AK001905 mRNA. Translation: BAA91971.1.
AK315641 mRNA. Translation: BAG38008.1.
AL049712 Genomic DNA. Translation: CAC01442.2.
AL049712 Genomic DNA. Translation: CAC01443.1.
CH471133 Genomic DNA. Translation: EAX10579.1.
CH471133 Genomic DNA. Translation: EAX10580.1.
CH471133 Genomic DNA. Translation: EAX10582.1.
CH471133 Genomic DNA. Translation: EAX10583.1.
BC001960 mRNA. Translation: AAH01960.1.
AL050094 mRNA. Translation: CAB43266.1.
CCDSCCDS13031.1. [O43837-2]
CCDS13032.1. [O43837-1]
PIRT08743.
T13147.
RefSeqNP_008830.2. NM_006899.3. [O43837-1]
NP_777280.1. NM_174855.2. [O43837-2]
UniGeneHs.436405.

3D structure databases

ProteinModelPortalO43837.
SMRO43837. Positions 47-382.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid109646. 7 interactions.
IntActO43837. 6 interactions.
MINTMINT-5003855.
STRING9606.ENSP00000370223.

Chemistry

DrugBankDB00157. NADH.

PTM databases

PhosphoSiteO43837.

Proteomic databases

MaxQBO43837.
PaxDbO43837.
PRIDEO43837.

Protocols and materials databases

DNASU3420.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000380843; ENSP00000370223; ENSG00000101365. [O43837-1]
ENST00000380851; ENSP00000370232; ENSG00000101365. [O43837-2]
GeneID3420.
KEGGhsa:3420.
UCSCuc002wgp.4. human. [O43837-1]
uc002wgq.4. human. [O43837-2]
uc002wgr.4. human. [O43837-3]

Organism-specific databases

CTD3420.
GeneCardsGC20M002639.
GeneReviewsIDH3B.
HGNCHGNC:5385. IDH3B.
HPAHPA049387.
HPA054180.
MIM604526. gene.
612572. phenotype.
neXtProtNX_O43837.
Orphanet791. Retinitis pigmentosa.
PharmGKBPA29633.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0473.
HOVERGENHBG052080.
InParanoidO43837.
KOK00030.
OMAILATPDY.
OrthoDBEOG75B85R.
PhylomeDBO43837.
TreeFamTF315033.

Enzyme and pathway databases

BioCycMetaCyc:ENSG00000101365-MONOMER.
ReactomeREACT_111217. Metabolism.
SABIO-RKO43837.

Gene expression databases

ArrayExpressO43837.
BgeeO43837.
CleanExHS_IDH3B.
GenevestigatorO43837.

Family and domain databases

Gene3D3.40.718.10. 1 hit.
InterProIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004434. Isocitrate_DH_NAD.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERPTHR11835. PTHR11835. 1 hit.
PfamPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsTIGR00175. mito_nad_idh. 1 hit.
PROSITEPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSIDH3B. human.
GeneWikiIDH3B.
GenomeRNAi3420.
NextBio13482.
PROO43837.
SOURCESearch...

Entry information

Entry nameIDH3B_HUMAN
AccessionPrimary (citable) accession number: O43837
Secondary accession number(s): B2RDR1 expand/collapse secondary AC list , D3DVX2, D3DVX3, O95106, Q5JXS8, Q9NQ06, Q9NQ07, Q9NUZ0, Q9UEX0, Q9UG99
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: May 1, 2007
Last modified: July 9, 2014
This is version 149 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM