RegulonDB RegulonDB 10.9: Gene Form
   

icd gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

icd ymfD rluE C0293 ArcA ArcA Cra anti-anti-terminator anti-terminator terminator TSS_1490 TSS_1490 TSS_1489 TSS_1489 TSS_1488 TSS_1488 TSS_1487 TSS_1487 TSS_1486 (cluster) TSS_1486 (cluster) TSS_1485 TSS_1485 TSS_1484 TSS_1484 TSS_1483 (cluster) TSS_1483 (cluster) TSS_1482 TSS_1482 icdAp1 icdAp1 TSS_1480 TSS_1480 icdAp2 icdAp2 TSS_1479 (cluster) TSS_1479 (cluster) nudJp6 nudJp6

Gene      
Name: icd    Texpresso search in the literature
Synonym(s): ECK1122, EG10489, b1136, icdA, icdE
Genome position(nucleotides): 1195123 --> 1196373 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.2
External database links:  
ASAP:
ABE-0003823
CGSC:
615
ECHOBASE:
EB0484
ECOLIHUB:
icd
ECOO157CYC:
ICDA
MIM:
147700
OU-MICROARRAY:
b1136
STRING:
511145.b1136
COLOMBOS: icd


Product      
Name: isocitrate dehydrogenase
Synonym(s): Icd, IcdA, IcdE
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 45.757
Isoelectric point: 4.902
Motif(s):
 
Type Positions Sequence
230 -> 230 K
339 -> 345 HGTAPKY
242 -> 242 K
29 -> 412 IPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAI
100 -> 100 K

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.4 - TCA cycle
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0004450 - isocitrate dehydrogenase (NADP+) activity
GO:0000287 - magnesium ion binding
GO:0051287 - NAD binding
biological_process GO:0006097 - glyoxylate cycle
GO:0006099 - tricarboxylic acid cycle
GO:0006979 - response to oxidative stress
GO:0022900 - electron transport chain
GO:0055114 - oxidation-reduction process
Reference(s): [1] Burke WF., et al., 1974
[2] Burke WF., et al., 1973
[3] Thorsness PE., et al., 1987
External database links:  
DIP:
DIP-10006N
ECOCYC:
ISOCITDEH-SUBUNIT
ECOLIWIKI:
b1136
INTERPRO:
IPR024084
INTERPRO:
IPR019818
INTERPRO:
IPR004439
MODBASE:
P08200
PANTHER:
PTHR43504
PDB:
1IDC
PDB:
1IDD
PDB:
1IDE
PDB:
1IDF
PDB:
1IKA
PDB:
1ISO
PDB:
1P8F
PDB:
1PB1
PDB:
1PB3
PDB:
1SJS
PDB:
3ICD
PDB:
3LCB
PDB:
4AJ3
PDB:
4AJA
PDB:
4AJB
PDB:
4AJC
PDB:
4AJR
PDB:
4AJS
PDB:
4BNP
PDB:
4ICD
PDB:
4P69
PDB:
5ICD
PDB:
6ICD
PDB:
7ICD
PDB:
8ICD
PDB:
9ICD
PDB:
1HJ6
PDB:
1GRP
PDB:
1GRO
PDB:
1CW7
PDB:
1CW4
PDB:
1CW1
PDB:
1BL5
PDB:
1AI3
PDB:
1AI2
PFAM:
PF00180
PRIDE:
P08200
PRODB:
PRO_000022989
PROSITE:
PS00470
REFSEQ:
NP_415654
SMART:
SM01329
SMR:
P08200
UNIPROT:
P08200


Operon      
Name: icd         
Operon arrangement:
Transcription unit        Promoter
icd
icd


Transcriptional Regulation      
Display Regulation             
Activated by: Cra
Repressed by: ArcA


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter nudJp6 1194437 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1479 (cluster) 1194944 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [5]
  promoter TSS_1480 1194970 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1482 1195013 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1483 (cluster) 1195019 forward For this promoter, there
Read more >
[RS-EPT-CBR] [5]
  promoter TSS_1484 1195022 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1485 1195033 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1486 (cluster) 1195396 forward For this promoter, there
Read more >
[RS-EPT-CBR] [5]
  promoter TSS_1487 1195466 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1488 1195945 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1489 1196007 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1490 1196016 forward nd [RS-EPT-CBR] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Burke WF., Johanson RA., Reeves HC., 1974, NADP+-specific isocitrate dehydrogenase of Escherichia coli. II. Subunit structure., Biochim Biophys Acta 351(2):333-40

 [2] Burke WF., Swafford JR., Reeves HC., 1973, Crystallization of NADP-specific isocitrate dehydrogenase., Science 181(4094):59-60

 [3] Thorsness PE., Koshland DE., 1987, Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate., J Biol Chem 262(22):10422-5

 [4] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


RegulonDB