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P39126 (IDH_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 121. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isocitrate dehydrogenase [NADP]

Short name=IDH
EC=1.1.1.42
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene names
Name:icd
Synonyms:citC
Ordered Locus Names:BSU29130
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length423 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.

Cofactor

Binds 1 magnesium or manganese ion per subunit By similarity.

Subunit structure

Homodimer. Ref.5

Miscellaneous

The enzyme can be phosphorylated in vitro by the E.coli isocitrate dehydrogenase kinase/phosphatase, but B.subtilis lacks such an enzyme.

Sequence similarities

Belongs to the isocitrate and isopropylmalate dehydrogenases family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

mdhP498143EBI-7829570,EBI-7827708

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 423423Isocitrate dehydrogenase [NADP]
PRO_0000083549

Regions

Nucleotide binding345 – 3517NADP By similarity

Sites

Metal binding3111Magnesium or manganese By similarity
Binding site951NADP By similarity
Binding site961Substrate
Binding site1041Substrate
Binding site1061Substrate
Binding site1101Substrate
Binding site1201Substrate By similarity
Binding site1441Substrate
Binding site3581NADP; via amide nitrogen and carbonyl oxygen By similarity
Binding site3971NADP By similarity
Binding site4011NADP By similarity
Site1511Critical for catalysis By similarity
Site2211Critical for catalysis By similarity

Secondary structure

............................................................................... 423
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P39126 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: CC69E694EB66D0D8

FASTA42346,418
        10         20         30         40         50         60 
MAQGEKITVS NGVLNVPNNP IIPFIEGDGT GPDIWNAASK VLEAAVEKAY KGEKKITWKE 

        70         80         90        100        110        120 
VYAGEKAYNK TGEWLPAETL DVIREYFIAI KGPLTTPVGG GIRSLNVALR QELDLFVCLR 

       130        140        150        160        170        180 
PVRYFTGVPS PVKRPEDTDM VIFRENTEDI YAGIEYAKGS EEVQKLISFL QNELNVNKIR 

       190        200        210        220        230        240 
FPETSGIGIK PVSEEGTSRL VRAAIDYAIE HGRKSVTLVH KGNIMKFTEG AFKNWGYELA 

       250        260        270        280        290        300 
EKEYGDKVFT WAQYDRIAEE QGKDAANKAQ SEAEAAGKII IKDSIADIFL QQILTRPNEF 

       310        320        330        340        350        360 
DVVATMNLNG DYISDALAAQ VGGIGIAPGA NINYETGHAI FEATHGTAPK YAGLDKVNPS 

       370        380        390        400        410        420 
SVILSGVLLL EHLGWNEAAD LVIKSMEKTI ASKVVTYDFA RLMDGATEVK CSEFGEELIK 


NMD 

« Hide

References

« Hide 'large scale' references
[1]"Identification of two distinct Bacillus subtilis citrate synthase genes."
Jin S., Sonenshein A.L.
J. Bacteriol. 176:4669-4679(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168 / SMY.
[2]"Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region."
Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.
Microbiology 143:3431-3441(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168.
[3]"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. expand/collapse author list , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 168.
[4]"Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/phosphatase."
Singh S.K., Miller S.P., Dean A., Banaszak L.J., LaPorte D.C.
J. Biol. Chem. 277:7567-7573(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION.
[5]"Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase."
Singh S.K., Matsuno K., LaPorte D.C., Banaszak L.J.
J. Biol. Chem. 276:26154-26163(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH CITRATE, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U05257 Genomic DNA. Translation: AAA96342.1.
AF008220 Genomic DNA. Translation: AAC00346.1.
AL009126 Genomic DNA. Translation: CAB14873.1.
PIRI40382.
RefSeqNP_390791.1. NC_000964.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1HQSX-ray1.55A/B1-423[»]
ProteinModelPortalP39126.
SMRP39126. Positions 1-423.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP39126. 2 interactions.
MINTMINT-1711252.
STRING224308.BSU29130.

PTM databases

PhosSiteP0204106.

Proteomic databases

PaxDbP39126.
PRIDEP39126.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB14873; CAB14873; BSU29130.
GeneID938183.
KEGGbsu:BSU29130.
PATRIC18977720. VBIBacSub10457_3048.

Organism-specific databases

GenoListBSU29130. [Micado]

Phylogenomic databases

eggNOGCOG0538.
HOGENOMHOG000021113.
KOK00031.
OMACLRPIRY.
OrthoDBEOG6SNDTP.
PhylomeDBP39126.

Enzyme and pathway databases

BioCycBSUB:BSU29130-MONOMER.

Family and domain databases

Gene3D3.40.718.10. 1 hit.
InterProIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERPTHR11835. PTHR11835. 1 hit.
PfamPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsTIGR00183. prok_nadp_idh. 1 hit.
PROSITEPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP39126.

Entry information

Entry nameIDH_BACSU
AccessionPrimary (citable) accession number: P39126
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList