Difference between revisions of "Sandbox"
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− | * '''Description:''' | + | * '''Description:''' "Catabolite repression HPr-like protein", Cofactor of the [[CcpA]] transcription factor<br/><br/> |
{| align="right" border="1" cellpadding="2" | {| align="right" border="1" cellpadding="2" | ||
|- | |- | ||
|style="background:#ABCDEF;" align="center"|'''Gene name''' | |style="background:#ABCDEF;" align="center"|'''Gene name''' | ||
− | |'' | + | |''crh'' |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | + | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcM'' |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Essential''' || no | + | |style="background:#ABCDEF;" align="center"| '''Essential''' || no |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Product''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || catabolite repression HPr-like protein |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || catabolite repression |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,2 kDa, 4.70 |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 255 bp, 85 amino acids |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcL]]'', ''[[yvcN]]'' |
|- | |- | ||
− | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS: | + | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15479]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
− | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |colspan="2" | '''Genetic context''' <br/> [[Image:crh_context.gif]] |
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | ||
|- | |- | ||
Line 35: | Line 35: | ||
=== Basic information === | === Basic information === | ||
− | * '''Locus tag:''' | + | * '''Locus tag:''' BSU34740 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
Line 41: | Line 41: | ||
=== Database entries === | === Database entries === | ||
− | * '''DBTBS entry:''' | + | * '''DBTBS entry:''' no entry |
− | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12403] |
=== Additional information=== | === Additional information=== | ||
− | |||
=The protein= | =The protein= | ||
Line 54: | Line 53: | ||
* '''Catalyzed reaction/ biological activity:''' | * '''Catalyzed reaction/ biological activity:''' | ||
− | * '''Protein family:''' | + | * '''Protein family:''' HPr family (according to Swiss-Prot) [[PtsH]],HPr family |
− | * '''Paralogous protein(s):''' | + | * '''Paralogous protein(s):''' [[PtsH |HPr]] |
=== Extended information on the protein === | === Extended information on the protein === | ||
Line 62: | Line 61: | ||
* '''Kinetic information:''' | * '''Kinetic information:''' | ||
− | * '''Domains:''' | + | * '''Domains:''' HPr domain (1–85) |
− | * '''Modification:''' | + | * '''Modification:''' phosphorylation on Ser46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed] |
* '''Cofactor(s):''' | * '''Cofactor(s):''' | ||
Line 70: | Line 69: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
− | * '''Interactions:''' [[ | + | * '''Interactions:''' Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed], Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed], [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed] |
* '''Localization:''' | * '''Localization:''' | ||
Line 76: | Line 75: | ||
=== Database entries === | === Database entries === | ||
− | * '''Structure:''' | + | * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2AK7 2AK7] (dimeric Crh-Ser46-P), [http://www.rcsb.org/pdb/explore.do?structureId=1ZVV 1ZVV] (CcpA-Crh-DNA complex), [http://www.rcsb.org/pdb/explore.do?structureId=2RLZ 2RLZ] (dimer), [http://www.rcsb.org/pdb/explore.do?structureId=1MU4 1MU4], [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=24634 NCBI], dimer [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=64943 NCBI], CcpA-Crh-DNA complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], dimeric phosphor-Crh [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39567 NCBI] |
+ | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06976 O06976] | ||
− | * ''' | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34740] |
− | + | === Additional information=== | |
− | |||
− | |||
− | + | Crh does not possess the phosphorylation site used for PTS phosphotransfer (His-15 in [[PtsH]]), it can only be phosphorylated on Ser-46 | |
=Expression and regulation= | =Expression and regulation= | ||
− | * '''Operon:''' ''[[ | + | * '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed] |
− | * ''' | + | * '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed] |
− | * '''Regulation:''' | + | * '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed] |
− | * '''Regulatory mechanism:''' | + | * '''Regulatory mechanism:''' |
− | * '''Additional information:''' | + | * '''Additional information:''' Crh is weakly expressed. This results in part from a poorly conserved ribosomal binding site of the mRNA. [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed] |
=Biological materials = | =Biological materials = | ||
− | * '''Mutant:''' | + | * '''Mutant:''' GP860 (aphA3), QB7097 (spc), available in [[Stülke]] lab |
− | * '''Expression vector:''' | + | * '''Expression vector:''' pGP41 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), pGP734 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Stülke]] lab |
− | + | ||
− | * '''lacZ fusion:''' | + | * '''lacZ fusion:''' see ''[[yvcI]]'' |
* '''GFP fusion:''' | * '''GFP fusion:''' | ||
− | * '''two-hybrid system:''' | + | * '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Boris Görke| Görke]] lab |
− | * '''Antibody:''' | + | * '''Antibody:''' available in [[Stülke]] lab (not very good) |
=Labs working on this gene/protein= | =Labs working on this gene/protein= | ||
+ | |||
+ | [[Boris Görke]], University of Göttingen, Germany | ||
+ | [http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage] | ||
+ | |||
+ | [[Anne Galinier]], University of Marseille, France | ||
+ | |||
+ | [[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage] | ||
+ | |||
+ | [[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage] | ||
=Your additional remarks= | =Your additional remarks= | ||
Line 118: | Line 125: | ||
=References= | =References= | ||
− | <pubmed> | + | <pubmed>12972249 9973552 9237995 16272399 15126459 10217795 17142398 16316990, </pubmed> |
− | # M | + | # Juy M, Penin F, Favier A (2003) Dimerization of Crh by reversible 3D domain swapping induces structural adjustments to its monomeric homologue Hpr. ''J Mol Biol.'' '''332(4):'''767-76. [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed] |
− | # | + | # Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the ''Bacillus subtilis xyn cre'' and catabolite repression of the ''xyn'' operon. J Mol Biol 1999, 286:307-314. [http://www.ncbi.nlm.nih.gov/sites/entrez/9973552 PubMed] |
+ | # Galinier, A., Haiech, J., Kilhoffer, M.-C., Jaquinod, M., Stülke, J., Deutscher, J., & Martin-Verstraete, I. (1997) The ''Bacillus subtilis crh'' gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA 94: 8439-8444. [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed] | ||
+ | # Görke et al. (2005) YvcK of ''Bacillus subtilis'' is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway. Microbiology 151: 3777-3791. [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed] | ||
+ | # Görke, B., Fraysse, L. & Galinier, A. Drastic differences in Crh and HPr synthesis levels reflect their different impacts on catabolite repression in ''Bacillus subtilis''. J. Bacteriol. 186, 2992-2995 (2004). [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed] | ||
+ | # Martin-Verstraete, I., Deutscher, J., and Galinier, A. (1999) Phosphorylation of HPr and Crh by HprK, early steps in the catabolite repression signalling pathway for the ''Bacillus subtilis'' levanase operon. J Bacteriol 181: 2966-2969. [http://www.ncbi.nlm.nih.gov/sites/entrez/10217795 PubMed] | ||
+ | # Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed] | ||
+ | # Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). [http://www.ncbi.nlm.nih.gov/sites/entrez/16316990 PubMed] |
Revision as of 14:13, 8 June 2009
- Description: "Catabolite repression HPr-like protein", Cofactor of the CcpA transcription factor
Gene name | crh |
Synonyms | yvcM |
Essential | no |
Product | catabolite repression HPr-like protein |
Function | catabolite repression |
MW, pI | 9,2 kDa, 4.70 |
Gene length, protein length | 255 bp, 85 amino acids |
Immediate neighbours | yvcL, yvcN |
Get the DNA and protein sequences (Barbe et al., 2009) | |
Genetic context ![]() This image was kindly provided by SubtiList
|
Contents
The gene
Basic information
- Locus tag: BSU34740
Phenotypes of a mutant
Database entries
- DBTBS entry: no entry
- SubtiList entry: [1]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity:
- Protein family: HPr family (according to Swiss-Prot) PtsH,HPr family
- Paralogous protein(s): HPr
Extended information on the protein
- Kinetic information:
- Domains: HPr domain (1–85)
- Cofactor(s):
- Effectors of protein activity:
- Localization:
Database entries
- Structure: 2AK7 (dimeric Crh-Ser46-P), 1ZVV (CcpA-Crh-DNA complex), 2RLZ (dimer), 1MU4, NCBI, dimer NCBI, CcpA-Crh-DNA complex NCBI, dimeric phosphor-Crh NCBI
- Swiss prot entry: O06976
- KEGG entry: [2]
Additional information
Crh does not possess the phosphorylation site used for PTS phosphotransfer (His-15 in PtsH), it can only be phosphorylated on Ser-46
Expression and regulation
- Regulation: very weak stimuation of expression by citrate and succinate PubMed
- Regulatory mechanism:
- Additional information: Crh is weakly expressed. This results in part from a poorly conserved ribosomal binding site of the mRNA. PubMed
Biological materials
- Mutant: GP860 (aphA3), QB7097 (spc), available in Stülke lab
- Expression vector: pGP41 (N-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP380), pGP734 (C-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP382), available in Stülke lab
- lacZ fusion: see yvcI
- GFP fusion:
- two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Görke lab
- Antibody: available in Stülke lab (not very good)
Labs working on this gene/protein
Boris Görke, University of Göttingen, Germany Homepage
Anne Galinier, University of Marseille, France
Wolfgang Hillen, Erlangen University, Germany Homepage
Richard Brennan, Houston, Texas, USA Homepage
Your additional remarks
References
- Juy M, Penin F, Favier A (2003) Dimerization of Crh by reversible 3D domain swapping induces structural adjustments to its monomeric homologue Hpr. J Mol Biol. 332(4):767-76. PubMed
- Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon. J Mol Biol 1999, 286:307-314. PubMed
- Galinier, A., Haiech, J., Kilhoffer, M.-C., Jaquinod, M., Stülke, J., Deutscher, J., & Martin-Verstraete, I. (1997) The Bacillus subtilis crh gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA 94: 8439-8444. PubMed
- Görke et al. (2005) YvcK of Bacillus subtilis is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway. Microbiology 151: 3777-3791. PubMed
- Görke, B., Fraysse, L. & Galinier, A. Drastic differences in Crh and HPr synthesis levels reflect their different impacts on catabolite repression in Bacillus subtilis. J. Bacteriol. 186, 2992-2995 (2004). PubMed
- Martin-Verstraete, I., Deutscher, J., and Galinier, A. (1999) Phosphorylation of HPr and Crh by HprK, early steps in the catabolite repression signalling pathway for the Bacillus subtilis levanase operon. J Bacteriol 181: 2966-2969. PubMed
- Pompeo et al. (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in Bacillus subtilis? J Bacteriol 189, 1154-1157.PubMed
- Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). PubMed