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| * '''Description:''' isocitrate dehydrogenase <br/><br/>
| | {{#bank: Icd}} |
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| {| align="right" border="1" cellpadding="2"
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| |style="background:#ABCDEF;" align="center"|'''Gene name'''
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| |''icd''
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| |-
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| |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citC ''
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| |-
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| |style="background:#ABCDEF;" align="center"| '''Essential''' || no
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| |-
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| |style="background:#ABCDEF;" align="center"| '''Product''' || isocitrate dehydrogenase
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| |-
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| |style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
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| |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29130 icd]
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| |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=Icd Icd]
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| |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=icd icd]'''
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| |-
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| |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46 kDa, 4.833
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| |-
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| |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1269 bp, 423 aa
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| |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mdh]], [[citZ]]''
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| |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29130 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29130 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29130 DNA_with_flanks]
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| |colspan="2" | '''Genetic context''' <br/> [[Image:icd_context.gif]]
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| <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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| |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=icd_2979716_2980987_-1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:icd_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29130]]
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| |-
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| |}
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| __TOC__
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| <br/><br/><br/><br/>
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| <br/><br/><br/><br/>
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| <br/><br/><br/><br/>
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| <br/><br/>
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|
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| = [[Categories]] containing this gene/protein =
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| {{SubtiWiki category|[[carbon core metabolism]]}},
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| {{SubtiWiki category|[[membrane proteins]]}},
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| {{SubtiWiki category|[[phosphoproteins]]}},
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| [[most abundant proteins]]
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| = This gene is a member of the following [[regulons]] =
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| {{SubtiWiki regulon|[[CcpA regulon]]}},
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| {{SubtiWiki regulon|[[CcpC regulon]]}}
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|
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| =The gene=
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| === Basic information ===
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| * '''Locus tag:''' BSU29130
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| ===Phenotypes of a mutant ===
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| ** reduced ability to sporulate [http://www.ncbi.nlm.nih.gov/pubmed/9244258 PubMed]
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| ** growth and sporulation defects of the mutant could be partially bypassed by deletion of the major citrate synthase gene (''[[citZ]]'') {{PubMed|10348849}}
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| === Database entries ===
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| * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29130&redirect=T BSU29130]
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| * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
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| * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10856]
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| === Additional information===
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| =The protein=
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| === Basic information/ Evolution ===
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| * '''Catalyzed reaction/ biological activity:''' Isocitrate + NADP<sup>+</sup> = 2-oxoglutarate + CO<sub>2</sub> + NADPH (according to Swiss-Prot)
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| * '''Protein family:''' isocitrate and isopropylmalate dehydrogenases family (according to Swiss-Prot)
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| * '''Paralogous protein(s):'''
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| === Extended information on the protein ===
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| * '''Kinetic information:'''
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| ** Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
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| ** specific activity: 1.64 µmol min<sup>-1</sup> (mg protein)<sup>-1</sup> {{PubMed|24571712}}
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| * '''[[Domains]]:'''
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| * '''Modification:'''
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| ** phosphorylated on Arg-180 {{PubMed|22517742}}
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| ** phosphorylated [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
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| ** ''in vitro'' phosphorylated by [[PrkC]] on Thr-138, Thr-147, and Thr-396 {{PubMed|20389117}}
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| * '''[[Cofactors]]:''' Mg<sup>2+</sup>, Mn<sup>2+</sup>, NADP<sup>+</sup>
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| * '''Effectors of protein activity:'''
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| ** Inhibited by glyoxylate, oxaloacetate and oxalomalate [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
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| *** Better inhibition when glyoxylate and oxaloacetate is combined, probably due to the non-enzymatic conversion into oxalomalate, which is a strong inhibitor [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
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| * '''[[SubtInteract|Interactions]]:'''
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| ** homodimer [http://www.ncbi.nlm.nih.gov/pubmed/11290745 PubMed]
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| ** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
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| ** [[Mdh]]-[[Icd]] {{PubMed|24325460}}
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| ** [[GltA]]-[[Icd]] {{PubMed|20933603}}
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| ** [[OdhB]]-[[Icd]] {{PubMed|20933603}}
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| * '''[[Localization]]:''' attached to the membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
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| === Database entries ===
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| * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29130&redirect=T BSU29130]
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| * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HQS 1HQS]
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| * '''UniProt:''' [http://www.uniprot.org/uniprot/P39126 P39126]
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| * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29130]
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| * '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.42 1.1.1.42]
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| === Additional information===
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| * This enzyme requires NADP+ exclusively. No activity was seen on the presence on NAD+ [http://www.ncbi.nlm.nih.gov/pubmed/4147570 PubMed]
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| * extensive information on the structure and enzymatic properties of Icd can be found at [http://www.proteopedia.org/wiki/index.php/Isocitrate_dehydrogenase Proteopedia]
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| =Expression and regulation=
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| * '''Operon:'''
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| **''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
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| **''[[icd]]-[[mdh]]'' {{PubMed|8045899}}
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| * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=icd_2979716_2980987_-1 icd] {{PubMed|22383849}}
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| * '''[[Sigma factor]]:'''
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| ** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
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| ** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}
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| * '''Regulation:'''
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| ** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
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| ** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
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| * '''Regulatory mechanism:'''
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| ** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
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| ** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
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| * '''Additional information:'''
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| ** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium): 37100 {{PubMed|24696501}}
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| ** number of protein molecules per cell (complex medium with amino acids, without glucose): 77080 {{PubMed|24696501}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 41324 {{PubMed|21395229}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 16631 {{PubMed|21395229}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 32135 {{PubMed|21395229}}
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| =Biological materials =
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| * '''Mutant:''' GP666 (spc), GP672 (erm), available in [[Jörg Stülke]]'s lab
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| ** 1A1000 ( ''icd''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A1000&Search=1A1000 BGSC]
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| ** 1A999 ( ''icd''::''spec''), {{PubMed| }}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A999&Search=1A999 BGSC]
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| ** GP790 (''[[citZ]]-[[icd]]-[[mdh]]''::''kan''), available in [[Jörg Stülke]]'s lab
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| * '''Expression vector:'''
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| ** pGP1121 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
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| * '''lacZ fusion:'''
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| * '''GFP fusion:'''
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| * '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
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| * '''Antibody:''' available in [[Linc Sonenshein]]'s lab
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| =Labs working on this gene/protein=
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| [[Linc Sonenshein| Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
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| =Your additional remarks=
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| =References=
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| <pubmed>10656796,12850135 11290745 10348849 11751849 18763711 17726680 16493705 4147570 20389117 9244258 20933603 22517742 24325460 24571712 15378759 24616559 </pubmed>
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| [[Category:Protein-coding genes]]
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