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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)DescriptionActionsGraphical viewLength
Binding sitei97SubstrateBy similarity1
Binding sitei107SubstrateBy similarity1
Binding sitei126SubstrateBy similarity1
Sitei133Critical for catalysisBy similarity1
Sitei196Critical for catalysisBy similarity1
Metal bindingi232Magnesium or manganeseBy similarity1
Binding sitei232SubstrateBy similarity1
Metal bindingi256Magnesium or manganeseBy similarity1
Metal bindingi260Magnesium or manganeseBy similarity1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00003103741 – 362Homoisocitrate dehydrogenaseAdd BLAST362

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei81Phosphoserine1 Publication1
Modified residuei91Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO14104.
PRIDEiO14104.

PTM databases

iPTMnetiO14104.

Interactioni

Protein-protein interaction databases

BioGridi279063. 19 interactors.
MINTiMINT-4670513.

Structurei

Secondary structure

1362
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 15Combined sources10
Helixi18 – 30Combined sources13
Helixi34 – 36Combined sources3
Beta strandi39 – 44Combined sources6
Helixi49 – 55Combined sources7
Helixi61 – 70Combined sources10
Beta strandi72 – 78Combined sources7
Helixi92 – 99Combined sources8
Beta strandi104 – 110Combined sources7
Beta strandi116 – 118Combined sources3
Beta strandi121 – 127Combined sources7
Helixi132 – 134Combined sources3
Beta strandi137 – 141Combined sources5
Beta strandi148 – 156Combined sources9
Helixi157 – 179Combined sources23
Beta strandi190 – 195Combined sources6
Turni197 – 199Combined sources3
Helixi203 – 214Combined sources12
Helixi215 – 217Combined sources3
Helixi219 – 221Combined sources3
Beta strandi224 – 230Combined sources7
Helixi231 – 240Combined sources10
Helixi242 – 244Combined sources3
Beta strandi246 – 250Combined sources5
Helixi252 – 263Combined sources12
Helixi264 – 266Combined sources3
Helixi269 – 271Combined sources3
Beta strandi275 – 277Combined sources3
Beta strandi282 – 284Combined sources3
Turni292 – 296Combined sources5
Helixi303 – 315Combined sources13
Helixi319 – 335Combined sources17
Helixi341 – 343Combined sources3
Helixi349 – 359Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TY3X-ray1.85A/B1-362[»]
3TY4X-ray1.55A/B1-362[»]
ProteinModelPortaliO14104.
SMRiO14104.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000021111.
InParanoidiO14104.
KOiK05824.
OMAiLMLEFMG.
OrthoDBiEOG092C2YAZ.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TY3X-ray1.85A/B1-362[»]
3TY4X-ray1.55A/B1-362[»]
ProteinModelPortaliO14104.
SMRiO14104.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi279063. 19 interactors.
MINTiMINT-4670513.

PTM databases

iPTMnetiO14104.

Proteomic databases

MaxQBiO14104.
PRIDEiO14104.

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.
OrthoDBiEOG092C2YAZ.
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...

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: November 2, 2016
This is version 107 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.