|
|
| (20 intermediate revisions by 6 users not shown) |
| Line 1: |
Line 1: |
| * '''Description:''' malate dehydrogenase <br/><br/>
| | {{#bank: Mdh}} |
|
| |
|
| {| align="right" border="1" cellpadding="2"
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"|'''Gene name'''
| |
| |''mdh''
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citH ''
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Essential''' || no
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Product''' || malate dehydrogenase
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
| |
| |-
| |
| |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU29120 mdh]
| |
| |-
| |
| |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Mdh Mdh]
| |
| |-
| |
| |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/> [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.727
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 936 bp, 312 aa
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phoP]], [[icd]]''
| |
| |-
| |
| |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14872]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
| |
| |-
| |
| |colspan="2" | '''Genetic context''' <br/> [[Image:mdh_context.gif]]
| |
| <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
| |
| |-
| |
| |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:mdh_expression.png|500px]]
| |
| |-
| |
| |}
| |
|
| |
| __TOC__
| |
| <br/><br/><br/><br/>
| |
| <br/><br/><br/><br/>
| |
| <br/><br/><br/><br/>
| |
| <br/><br/>
| |
|
| |
| = [[Categories]] containing this gene/protein =
| |
| {{SubtiWiki category|[[carbon core metabolism]]}},
| |
| {{SubtiWiki category|[[membrane proteins]]}},
| |
| {{SubtiWiki category|[[phosphoproteins]]}}
| |
|
| |
| = This gene is a member of the following [[regulons]] =
| |
| {{SubtiWiki regulon|[[CcpA regulon]]}},
| |
| {{SubtiWiki regulon|[[CcpC regulon]]}}
| |
|
| |
| =The gene=
| |
|
| |
| === Basic information ===
| |
|
| |
| * '''Locus tag:''' BSU29120
| |
|
| |
| ===Phenotypes of a mutant ===
| |
|
| |
| === Database entries ===
| |
|
| |
| * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citZ-icd-mdh.html]
| |
|
| |
| * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11386]
| |
|
| |
| === Additional information===
| |
|
| |
|
| |
|
| |
|
| |
| =The protein=
| |
|
| |
| === Basic information/ Evolution ===
| |
|
| |
| * '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = oxaloacetate + NADH (according to Swiss-Prot)
| |
|
| |
| * '''Protein family:''' MDH type 3 family (according to Swiss-Prot)
| |
|
| |
| * '''Paralogous protein(s):'''
| |
|
| |
| === Extended information on the protein ===
| |
|
| |
| * '''Kinetic information:''' Reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
| |
|
| |
| * '''Domains:'''
| |
|
| |
| * '''Modification:'''
| |
| ** phosphorylated on Arg-156 {{PubMed|22517742}}
| |
| ** phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
| |
|
| |
| * '''Cofactor(s):'''
| |
|
| |
| * '''Effectors of protein activity:'''
| |
| ** Inhibited by Mg2+, Ca2+, Zn2+, Ag2+ and Hg2+ [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed] [http://www.ncbi.nlm.nih.gov/pubmed/922015 PubMed]
| |
| ** Inhibited by oxaloacetate (above 1mM) and malate (above 7,7mM) [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
| |
|
| |
| * '''[[SubtInteract|Interactions]]:'''
| |
| ** [[CitZ]]-[[Mdh]]-[[Icd]] (this is the core of the TCA cycle metabolon) {{PubMed|20933603}}
| |
| ** [[Mdh]]-[[PckA]] (this interaction occurs under gluconeogenic, but not under glycolytic conditions) {{PubMed|20933603}}
| |
| ** [[Mdh]]-[[Ndh]] {{PubMed|20933603}}
| |
| ** [[Mdh]]-[[CitB]] {{PubMed|20933603}}
| |
| ** [[Mdh]]-[[CitG]] {{PubMed|20933603}}
| |
| ** [[Mdh]]-[[SucC]] {{PubMed|20933603}}
| |
|
| |
| * '''[[Localization]]:''' cytoplasm (according to Swiss-Prot), membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
| |
|
| |
| === Database entries ===
| |
|
| |
| * '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1EMD 1EMD] (''E.coli'')
| |
|
| |
| * '''UniProt:''' [http://www.uniprot.org/uniprot/P49814 P49814]
| |
|
| |
| * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29120]
| |
|
| |
| * '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.37 1.1.1.37]
| |
|
| |
| === Additional information===
| |
| * The enzyme is a tetramer [http://www.ncbi.nlm.nih.gov/pubmed/14284712 PubMed]
| |
| * extensive information on the structure and enzymatic properties of Mdh can be found at [http://www.proteopedia.org/wiki/index.php/Malate_dehydrogenase Proteopedia]
| |
|
| |
| =Expression and regulation=
| |
| * '''Operon:'''
| |
| **''[[citZ]]-[[icd]]-[[mdh]]'' {{PubMed|8045899}}
| |
| **''[[icd]]-[[mdh]]'' {{PubMed|8045899}}
| |
|
| |
| * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mdh_2978734_2979672_-1 mdh] {{PubMed|22383849}}
| |
|
| |
| * '''Sigma factor:'''
| |
| ** ''[[citZ]]'': [[SigA]] {{PubMed|8045899}}
| |
| ** ''[[icd]]'': [[SigA]] {{PubMed|8045899}}
| |
|
| |
| * '''Regulation:'''
| |
| ** ''[[citZ]]'': catabolite repression ([[CcpA]]) {{PubMed|12100558}}
| |
| ** ''[[citZ]]'': repression by glucose + glutamate ([[CcpC]]) {{PubMed|12100558}}
| |
| ** ''[[mdh]]'': constitutive
| |
|
| |
| * '''Regulatory mechanism:'''
| |
| ** [[CcpA]]: transcription repression, [[CcpC]]: transcription repression {{PubMed|12100558}}
| |
| ** [[CcpC]]: transcription repression (molecular inducer: citrate) [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
| |
|
| |
| * '''Additional information:'''
| |
|
| |
| =Biological materials =
| |
|
| |
| * '''Mutant:''' GP719(spc) & GP1150(spc), available in [[Stülke]] lab
| |
|
| |
| * '''Expression vector:'''
| |
| ** pGP1123 (N-terminal Strep-tag, for [[SPINE]], purification from ''B. subtilis'', in [[pGP380]]) (available in [[Jörg Stülke]]'s lab)
| |
| ** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP385, available in [[Jörg Stülke]]'s lab
| |
| ** pGP1755 (expression / purification of Mdh-S149A, with N-terminal His-tag from ''E. coli'', in [[pWH844]]), available in [[Jörg Stülke]]'s lab
| |
| ** pGP1764 (for expression, purification in ''E. coli'' with N-terminal Strep-tag, in [[pGP172]], available in [[Jörg Stülke]]'s lab)
| |
|
| |
| * '''lacZ fusion:'''
| |
|
| |
| * '''GFP fusion:'''
| |
|
| |
| * '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Jörg Stülke]]'s lab
| |
|
| |
| * '''Antibody:'''
| |
|
| |
| * '''FLAG-tag construct:'''
| |
| ** GP1130 (spc, based on [[pGP1331]]), available in [[Jörg Stülke]]'s lab
| |
|
| |
| =Labs working on this gene/protein=
| |
|
| |
| =Your additional remarks=
| |
|
| |
| =References=
| |
|
| |
| <pubmed>10656796,18763711 14284712 922015 12100558 17218307 8550482 8045899 20933603 22517742</pubmed>
| |
|
| |
| [[Category:Protein-coding genes]]
| |
