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P16100

- IDH_AZOVI

UniProt

P16100 - IDH_AZOVI

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Protein

Isocitrate dehydrogenase [NADP]

Gene

icd

Organism
Azotobacter vinelandii
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Binds 1 magnesium or manganese ion per subunit.

Enzyme regulationi

Inhibition of this enzyme by phosphorylation regulates the branch point between the Krebs cycle and the glyoxylate bypass, which is an alternate route that accumulates carbon for biosynthesis when acetate is the sole carbon source for growth. The phosphorylation state of this enzyme is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK).

Temperature dependencei

Optimum temperature is above 40 degrees Celsius.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei135 – 1351NADP
Binding sitei145 – 1451Substrate
Sitei255 – 2551Critical for catalysisBy similarity
Metal bindingi350 – 3501Magnesium or manganese
Sitei420 – 4201Critical for catalysisBy similarity
Binding sitei547 – 5471Substrate
Metal bindingi548 – 5481Magnesium or manganese
Metal bindingi552 – 5521Magnesium or manganeseBy similarity
Binding sitei589 – 5891NADP
Binding sitei649 – 6491NADP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi82 – 876NADP
Nucleotide bindingi584 – 5852NADP
Nucleotide bindingi600 – 6023NADP

GO - Molecular functioni

  1. isocitrate dehydrogenase (NADP+) activity Source: UniProtKB-EC
  2. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. glyoxylate cycle Source: UniProtKB-KW
  2. tricarboxylic acid cycle Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glyoxylate bypass, Tricarboxylic acid cycle

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NADP

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-13167.

Names & Taxonomyi

Protein namesi
Recommended name:
Isocitrate dehydrogenase [NADP] (EC:1.1.1.42)
Short name:
IDH
Alternative name(s):
Oxalosuccinate decarboxylase
Gene namesi
Name:icd
OrganismiAzotobacter vinelandii
Taxonomic identifieri354 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 741740Isocitrate dehydrogenase [NADP]PRO_0000083593Add
BLAST

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiP16100.

Interactioni

Subunit structurei

Monomer.1 Publication

Structurei

Secondary structure

1
741
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 106
Helixi13 – 3119
Turni32 – 343
Beta strandi36 – 416
Helixi44 – 518
Helixi53 – 553
Turni58 – 603
Helixi65 – 728
Beta strandi79 – 824
Helixi90 – 10213
Helixi117 – 12913
Beta strandi130 – 1323
Helixi135 – 1384
Beta strandi143 – 1464
Helixi149 – 1579
Beta strandi172 – 1743
Beta strandi177 – 1804
Helixi181 – 1844
Beta strandi186 – 1894
Beta strandi192 – 20211
Beta strandi207 – 21610
Beta strandi221 – 2277
Helixi229 – 24618
Beta strandi249 – 2524
Turni256 – 2583
Helixi262 – 27413
Helixi276 – 2816
Helixi283 – 2886
Helixi293 – 2953
Helixi297 – 3037
Helixi304 – 3063
Helixi309 – 32517
Beta strandi331 – 3333
Turni334 – 3374
Turni340 – 3423
Beta strandi346 – 3483
Helixi349 – 35810
Turni359 – 3613
Beta strandi362 – 3643
Beta strandi368 – 3769
Helixi380 – 39617
Turni401 – 4033
Beta strandi409 – 4113
Turni414 – 4163
Helixi418 – 4214
Helixi423 – 4253
Beta strandi426 – 4283
Beta strandi430 – 43910
Beta strandi444 – 4507
Beta strandi455 – 4617
Helixi463 – 48018
Beta strandi484 – 4874
Helixi493 – 50614
Beta strandi516 – 5194
Helixi521 – 53313
Beta strandi539 – 5424
Helixi544 – 55916
Beta strandi562 – 57110
Beta strandi576 – 5805
Helixi587 – 59610
Helixi604 – 62017
Helixi624 – 64219
Beta strandi649 – 6535
Helixi656 – 67318
Helixi678 – 69316
Helixi695 – 7039
Beta strandi706 – 7083
Beta strandi715 – 7173
Helixi720 – 7278
Helixi731 – 7366
Turni737 – 7393

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1ITWX-ray1.95A/B/C/D1-741[»]
1J1WX-ray3.20A/B/C/D1-741[»]
ProteinModelPortaliP16100.
SMRiP16100. Positions 2-741.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16100.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni132 – 1398Substrate binding

Domaini

This molecule consists of two distinct domains, a small domain and a large domain. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.

Sequence similaritiesi

Belongs to the monomeric-type IDH family.Curated

Family and domain databases

Gene3Di3.40.718.10. 3 hits.
InterProiIPR004436. Isocitrate_DH_NADP_mono.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PfamiPF03971. IDH. 1 hit.
[Graphical view]
PIRSFiPIRSF009407. IDH_monmr. 1 hit.
TIGRFAMsiTIGR00178. monomer_idh. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P16100-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSTPKIIYTL TDEAPALATY SLLPIIKAFT GSSGIAVETR DISLAGRLIA
60 70 80 90 100
TFPEYLTDTQ KISDDLAELG KLATTPDANI IKLPNISASV PQLKAAIKEL
110 120 130 140 150
QQQGYKLPDY PEEPKTDTEK DVKARYDKIK GSAVNPVLRE GNSDRRAPLS
160 170 180 190 200
VKNYARKHPH KMGAWSADSK SHVAHMDNGD FYGSEKAALI GAPGSVKIEL
210 220 230 240 250
IAKDGSSTVL KAKTSVQAGE IIDSSVMSKN ALRNFIAAEI EDAKKQGVLL
260 270 280 290 300
SVHLKATMMK VSDPIMFGQI VSEFYKDALT KHAEVLKQIG FDVNNGIGDL
310 320 330 340 350
YARIKTLPEA KQKEIEADIQ AVYAQRPQLA MVNSDKGITN LHVPSDVIVD
360 370 380 390 400
ASMPAMIRDS GKMWGPDGKL HDTKAVIPDR CYAGVYQVVI EDCKQHGAFD
410 420 430 440 450
PTTMGSVPNV GLMAQKAEEY GSHDKTFQIP ADGVVRVTDE SGKLLLEQSV
460 470 480 490 500
EAGDIWRMCQ AKDAPIQDWV KLAVNRARAT NTPAVFWLDP ARAHDAQVIA
510 520 530 540 550
KVERYLKDYD TSGLDIRILS PVEATRFSLA RIREGKDTIS VTGNVLRDYL
560 570 580 590 600
TDLFPIMELG TSAKMLSIVP LMSGGGLFET GAGGSAPKHV QQFLEEGYLR
610 620 630 640 650
WDSLGEFLAL AASLEHLGNA YKNPKALVLA STLDQATGKI LDNNKSPARK
660 670 680 690 700
VGEIDNRGSH FYLALYWAQA LAAQTEDKEL QAQFTGIAKA LTDNETKIVG
710 720 730 740
ELAAAQGKPV DIAGYYHPNT DLTSKAIRPS ATFNAALAPL A
Length:741
Mass (Da):80,390
Last modified:January 23, 2007 - v5
Checksum:i29FF35278E5AED8B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D73443 Genomic DNA. Translation: BAA11169.1.
PIRiA10759.
JC7822.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
D73443 Genomic DNA. Translation: BAA11169.1 .
PIRi A10759.
JC7822.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1ITW X-ray 1.95 A/B/C/D 1-741 [» ]
1J1W X-ray 3.20 A/B/C/D 1-741 [» ]
ProteinModelPortali P16100.
SMRi P16100. Positions 2-741.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi P16100.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

BioCyci MetaCyc:MONOMER-13167.

Miscellaneous databases

EvolutionaryTracei P16100.

Family and domain databases

Gene3Di 3.40.718.10. 3 hits.
InterProi IPR004436. Isocitrate_DH_NADP_mono.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view ]
Pfami PF03971. IDH. 1 hit.
[Graphical view ]
PIRSFi PIRSF009407. IDH_monmr. 1 hit.
TIGRFAMsi TIGR00178. monomer_idh. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Cloning, sequencing, and expression of a gene encoding the monomeric isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter vinelandii."
    Sahara T., Takada Y., Takeuchi Y., Yamaoka N., Fukunaga N.
    Biosci. Biotechnol. Biochem. 66:489-500(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-16.
  2. "Triphosphopyridine nucleotide specific isocitrate dehydrogenase from Azotobacter vinelandii. Alkylation of a specific methionine residue and amino acid sequence of the peptide containing this residue."
    Edwards D.J., Heinrikson R.L., Chung A.E.
    Biochemistry 13:677-683(1974) [PubMed] [Europe PMC] [Abstract]
    Cited for: PRELIMINARY PROTEIN SEQUENCE OF 229-251 AND 255-260.
  3. "Structure of the monomeric isocitrate dehydrogenase: evidence of a protein monomerization by a domain duplication."
    Yasutake Y., Watanabe S., Yao M., Takada Y., Fukunaga N., Tanaka I.
    Structure 10:1637-1648(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEXES WITH ISOCITRATE; MANGANESE AND NADP, SUBUNIT.

Entry informationi

Entry nameiIDH_AZOVI
AccessioniPrimary (citable) accession number: P16100
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: January 23, 2007
Last modified: October 29, 2014
This is version 98 of the entry and version 5 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3