Revision as of 13:31, 8 June 2009

Description: pyruvate kinase, glycolytic enzyme

Gene name	pyk
Synonyms	pykA
Essential	no
Product	pyruvate kinase
Function	catabolic enzyme in glycolysis
MW, pI	61,9 kDa, 4.88
Gene length, protein length	1755 bp, 585 amino acids
Immediate neighbours	pfkA, ytzA
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList

The gene

Basic information

Locus tag: BSU29180

Phenotypes of a mutant

Unable to grow with non-PTS carbohydrates (such as glucitol or glycerol) as single carbon source.

Database entries

DBTBS entry: [1]

SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

Catalyzed reaction/ biological activity: ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions

Protein family: PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)

Paralogous protein(s):

Extended information on the protein

Kinetic information:

Domains:

Modification: phosphorylation on Ser36 PubMed, PubMed, phosphorylation on Ser536 or Ser546 PubMed

Cofactor(s): magnesium ion, potassium

Effectors of protein activity: activated by PEP PubMed

Interactions:

Localization: cytoplasm PubMed

Database entries

Structure: 2E28 (Geobacillus stearothermophilus), 2E28 (from Geobacillus stearothermophilus) NCBI

Swiss prot entry: [3]

KEGG entry: [4]

E.C. number: 2.7.1.40

Additional information

Expression and regulation

Operon: pfkA pyk PubMed

Sigma factor:

Regulation: twofold induced by glucose PubMed

Regulatory mechanism:

Additional information:

Biological materials

Mutant: GP590 (cat), available in Stülke lab

Expression vector:

Expression in E. coli, N-terminal His-tag: pGP1100 (in pWH844), available in Stülke lab

Expression in B. subtilis, native protein: pGP1411 (in pBQ200), available in Stülke lab

Expression in B. subtilis, N-terminal Strep-tag: pGP1409 (in pGP380), available in Stülke lab

Expression in B. subtilis, C-terminal Strep-tag: pGP1410 (in pGP382), available in Stülke lab

lacZ fusion: see pfkA

GFP fusion:

two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

Antibody:

Labs working on this gene/protein

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis. Proteomics 7: 3509-3526. PubMed
Lévine et al. (2006) Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. Proteomics 6: 2157-2173 PubMed
Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon. Mol Microbiol 41, 409-422.PubMed
Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. PubMed
Fry, B., Zhu, T., Domach, M. M., Koepsel, R. R., Phalakornkule, C., and Ataai, M. M. (2000) Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant. Appl Env Microbiol 66: 4045-4049. PubMed
Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed

@@ Line 1: / Line 1: @@
-* '''Description:''' phosphoribosylformylglycinamidine synthase <br/><br/>
+* '''Description:''' pyruvate kinase, glycolytic enzyme <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''purQ''
+|''pyk''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''pykA''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || phosphoribosylformylglycinamidine synthase
+|style="background:#ABCDEF;" align="center"| '''Product''' || pyruvate kinase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || purine biosynthesis
+|style="background:#ABCDEF;" align="center"|'''Function''' || catabolic enzyme in glycolysis
 |-
-|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 24 kDa, 4.627
+|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61,9 kDa, 4.88
 |-
-|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 681 bp, 227 aa
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1755 bp, 585 amino acids
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[purS]]'', ''[[purL]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pfkA]]'', ''[[ytzA]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12467&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14878&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 |-
-|-
+|colspan="2" | '''Genetic context''' <br/> [[Image:pyk_context.gif]]
-|-
-|colspan="2" | '''Genetic context''' <br/> [[Image:purQ_context.gif]]
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
@@ Line 37: / Line 35: @@
 === Basic information ===
-* '''Locus tag:''' BSU06470
+* '''Locus tag:''' BSU29180
 ===Phenotypes of a mutant ===
+Unable to grow with non-PTS carbohydrates (such as glucitol or  glycerol) as single carbon source.
 === Database entries ===
-* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purEKBCSQLFMNHD.html]
+* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/pfkA-pyk-ytzA.html]
-* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10706]
+* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12661]
 === Additional information===
 =The protein=
@@ Line 54: / Line 53: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' ATP + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H<sub>2</sub>O = ADP + phosphate + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate (according to Swiss-Prot)
+* '''Catalyzed reaction/ biological activity:''' ADP + phosphoenolpyruvate --> ATP + pyruvate, the reaction is irreversible under physiological conditions
-* '''Protein family:'''
+* '''Protein family:''' PEP-utilizing enzyme family (according to Swiss-Prot) pyruvate kinase family, (C-terminal section: PEP-utilizing enzyme family)
 * '''Paralogous protein(s):'''
@@ Line 66: / Line 65: @@
 * '''Domains:'''
-* '''Modification:'''
+* '''Modification:''' phosphorylation on Ser36 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], phosphorylation on Ser536 or Ser546 [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
-* '''Cofactor(s):'''
+* '''Cofactor(s):''' magnesium ion, potassium
-* '''Effectors of protein activity:'''
+* '''Effectors of protein activity:''' activated by PEP [http://www.ncbi.nlm.nih.gov/sites/entrez/4623707 PubMed]
-* '''Interactions:''' [[PurS]]-[[PurQ]]-[[PurL]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15301530 PubMed]
+* '''Interactions:'''
-* '''Localization:''' cytoplasm (according to Swiss-Prot)
+* '''Localization:''' cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 === Database entries ===
-* '''Structure:'''
+* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2E28 2E28] (Geobacillus stearothermophilus), 	2E28 (from ''Geobacillus stearothermophilus'') [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=62183 NCBI]
-* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P12041 P12041]
+* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P80885]
-* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU06470]
+* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU29180]
-* '''E.C. number:''' [http://www.expasy.org/enzyme/6.3.5.3 6.3.5.3]
+* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.40 2.7.1.40]
 === Additional information===
-:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
 =Expression and regulation=
-* '''Operon:''' ''[[purE]]-[[purK]]-[[purB]]-[[purC]]-[[purS]]-[[purQ]]-[[purL]]-[[purF]]-[[purM]]-[[purN]]-[[purH]]-[[purD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
+* '''Operon:''' ''[[pfkA]] [[pyk]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
-* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
+* '''Sigma factor:'''
-* '''Regulation:'''
+* '''Regulation:''' twofold induced by glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
-** repressed in the presence of adenine or adenosine([[PurR]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
-** repressed in the presence of guanine([[G-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed]
-** expression activated by glucose (4.4 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 * '''Regulatory mechanism:'''
-** [[PurR]]: transcription repression (molecular inducer: PRPP) [http://www.ncbi.nlm.nih.gov/sites/entrez/2536750 PubMed]
-** [[G-box]]: transcription termination/ antitermination ([[riboswitch]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/3036807 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/12787499 PubMed2]
-* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+* '''Additional information:'''
 =Biological materials =
-* '''Mutant:'''
+* '''Mutant:''' GP590 (cat), available in [[Stülke]] lab
+* '''Expression vector:'''
+Expression in ''E. coli'', N-terminal His-tag: pGP1100 (in [[pWH844]]), available in [[Stülke]] lab
-* '''Expression vector:'''
+Expression in ''B. subtilis'', native protein: pGP1411 (in [[pBQ200]]), available in [[Stülke]] lab
-* '''lacZ fusion:'''
+Expression in ''B. subtilis'', N-terminal Strep-tag: pGP1409 (in [[pGP380]]), available in [[Stülke]] lab
+Expression in ''B. subtilis'', C-terminal Strep-tag: pGP1410 (in [[pGP382]]), available in [[Stülke]] lab
+* '''lacZ fusion:''' see ''[[pfkA]]''
 * '''GFP fusion:'''
-* '''two-hybrid system:'''
+* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
 * '''Antibody:'''
 =Labs working on this gene/protein=
+[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 =Your additional remarks=
@@ Line 126: / Line 129: @@
 =References=
-<pubmed>12850135, </pubmed>
+<pubmed>17726680 16493705 11489127 17505547 10966427 17218307, </pubmed>
-# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
+# Eymann et al. (2007) Dynamics of protein phosphorylation on Ser/Thr/Tyr in ''Bacillus subtilis''. ''Proteomics'' '''7:''' 3509-3526. [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
-# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+# L&#233;vine et al. (2006) Analysis of the dynamic ''Bacillus subtilis'' Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes. ''Proteomics'' '''6:''' 2157-2173 [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed]
-# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+# Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in ''Bacillus subtilis'': evidence for the presence of multiple levels of control of the ''gapA'' operon. Mol Microbiol 41, 409-422.[http://www.ncbi.nlm.nih.gov/sites/entrez/11489127 PubMed]
+# Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. [http://www.ncbi.nlm.nih.gov/sites/entrez/17505547 PubMed]
+# Fry, B., Zhu, T., Domach, M. M., Koepsel, R. R., Phalakornkule, C., and Ataai, M. M. (2000) Characterization of growth and acid formation in a Bacillus subtilis pyruvate kinase mutant. Appl Env Microbiol 66: 4045-4049. [http://www.ncbi.nlm.nih.gov/sites/entrez/10966427 PubMed]
+# Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model  bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707  [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]