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Protein

Homoisocitrate dehydrogenase

Gene

lys12

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

Pathwayi: L-lysine biosynthesis via AAA pathway

This protein is involved in step 4 of the subpathway that synthesizes L-alpha-aminoadipate from 2-oxoglutarate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Homocitrate synthase, mitochondrial (lys4)
  2. Homocitrate dehydratase, mitochondrial (SPBP4H10.15)
  3. Homoaconitase, mitochondrial (lys2)
  4. Homoisocitrate dehydrogenase (lys12)
  5. no protein annotated in this organism
This subpathway is part of the pathway L-lysine biosynthesis via AAA pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-alpha-aminoadipate from 2-oxoglutarate, the pathway L-lysine biosynthesis via AAA pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei97 – 971SubstrateBy similarity
Binding sitei107 – 1071SubstrateBy similarity
Binding sitei126 – 1261SubstrateBy similarity
Sitei133 – 1331Critical for catalysisBy similarity
Sitei196 – 1961Critical for catalysisBy similarity
Metal bindingi232 – 2321Magnesium or manganeseBy similarity
Binding sitei232 – 2321SubstrateBy similarity
Metal bindingi256 – 2561Magnesium or manganeseBy similarity
Metal bindingi260 – 2601Magnesium or manganeseBy similarity

GO - Molecular functioni

GO - Biological processi

  • lysine biosynthetic process Source: PomBase
  • lysine biosynthetic process via aminoadipic acid Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD

Enzyme and pathway databases

UniPathwayiUPA00033; UER00030.

Names & Taxonomyi

Protein namesi
Recommended name:
Homoisocitrate dehydrogenase (EC:1.1.1.87)
Short name:
HICDH
Gene namesi
Name:lys12
ORF Names:SPAC31G5.04
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC31G5.04.
PomBaseiSPAC31G5.04. lys12.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: PomBase
  • mitochondrion Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 362362Homoisocitrate dehydrogenasePRO_0000310374Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei81 – 811Phosphoserine1 Publication
Modified residuei91 – 911Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO14104.

PTM databases

iPTMnetiO14104.

Interactioni

Protein-protein interaction databases

BioGridi279063. 19 interactions.
MINTiMINT-4670513.

Structurei

Secondary structure

1
362
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 1510Combined sources
Helixi18 – 3013Combined sources
Helixi34 – 363Combined sources
Beta strandi39 – 446Combined sources
Helixi49 – 557Combined sources
Helixi61 – 7010Combined sources
Beta strandi72 – 787Combined sources
Helixi92 – 998Combined sources
Beta strandi104 – 1107Combined sources
Beta strandi116 – 1183Combined sources
Beta strandi121 – 1277Combined sources
Helixi132 – 1343Combined sources
Beta strandi137 – 1415Combined sources
Beta strandi148 – 1569Combined sources
Helixi157 – 17923Combined sources
Beta strandi190 – 1956Combined sources
Turni197 – 1993Combined sources
Helixi203 – 21412Combined sources
Helixi215 – 2173Combined sources
Helixi219 – 2213Combined sources
Beta strandi224 – 2307Combined sources
Helixi231 – 24010Combined sources
Helixi242 – 2443Combined sources
Beta strandi246 – 2505Combined sources
Helixi252 – 26312Combined sources
Helixi264 – 2663Combined sources
Helixi269 – 2713Combined sources
Beta strandi275 – 2773Combined sources
Beta strandi282 – 2843Combined sources
Turni292 – 2965Combined sources
Helixi303 – 31513Combined sources
Helixi319 – 33517Combined sources
Helixi341 – 3433Combined sources
Helixi349 – 35911Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TY3X-ray1.85A/B1-362[»]
3TY4X-ray1.55A/B1-362[»]
ProteinModelPortaliO14104.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000021111.
InParanoidiO14104.
KOiK05824.
OMAiLMLEFMG.
OrthoDBiEOG7R83BB.
PhylomeDBiO14104.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O14104-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSATRRIVLG LIPADGIGKE VVPAARRLME NLPAKHKLKF DFIDLDAGWG
60 70 80 90 100
TFERTGKALP ERTVERLKTE CNAALFGAVQ SPTHKVAGYS SPIVALRKKM
110 120 130 140 150
GLYANVRPVK SLDGAKGKPV DLVIVRENTE CLYVKEERMV QNTPGKRVAE
160 170 180 190 200
AIRRISEEAS TKIGKMAFEI AKSRQKIRES GTYSIHKKPL VTIIHKSNVM
210 220 230 240 250
SVTDGLFRES CRHAQSLDPS YASINVDEQI VDSMVYRLFR EPECFDVVVA
260 270 280 290 300
PNLYGDILSD GAASLIGSLG LVPSANVGDN FVMSEPVHGS APDIAGRGIA
310 320 330 340 350
NPVATFRSVA LMLEFMGHQD AAADIYTAVD KVLTEGKVLT PDLGGKSGTN
360
EITDAVLANI HN
Length:362
Mass (Da):39,256
Last modified:January 1, 1998 - v1
Checksum:i85865AFD69BCE773
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB11688.1.
PIRiT38621.
RefSeqiNP_594004.1. NM_001019430.2.

Genome annotation databases

EnsemblFungiiSPAC31G5.04.1; SPAC31G5.04.1:pep; SPAC31G5.04.
GeneIDi2542609.
KEGGispo:SPAC31G5.04.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB11688.1.
PIRiT38621.
RefSeqiNP_594004.1. NM_001019430.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3TY3X-ray1.85A/B1-362[»]
3TY4X-ray1.55A/B1-362[»]
ProteinModelPortaliO14104.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi279063. 19 interactions.
MINTiMINT-4670513.

PTM databases

iPTMnetiO14104.

Proteomic databases

MaxQBiO14104.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC31G5.04.1; SPAC31G5.04.1:pep; SPAC31G5.04.
GeneIDi2542609.
KEGGispo:SPAC31G5.04.

Organism-specific databases

EuPathDBiFungiDB:SPAC31G5.04.
PomBaseiSPAC31G5.04. lys12.

Phylogenomic databases

HOGENOMiHOG000021111.
InParanoidiO14104.
KOiK05824.
OMAiLMLEFMG.
OrthoDBiEOG7R83BB.
PhylomeDBiO14104.

Enzyme and pathway databases

UniPathwayiUPA00033; UER00030.

Miscellaneous databases

PROiO14104.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
InterProiIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERiPTHR11835. PTHR11835. 1 hit.
PfamiPF00180. Iso_dh. 1 hit.
[Graphical view]
SMARTiSM01329. Iso_dh. 1 hit.
[Graphical view]
PROSITEiPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-81 AND SER-91, IDENTIFICATION BY MASS SPECTROMETRY.
  4. "Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe."
    Bulfer S.L., Hendershot J.M., Trievel R.C.
    Proteins 80:661-666(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS).

Entry informationi

Entry nameiLYS12_SCHPO
AccessioniPrimary (citable) accession number: O14104
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 13, 2007
Last sequence update: January 1, 1998
Last modified: June 8, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.