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Escherichia coli K-12 substr. MG1655 Enzyme: glycine decarboxylase



Gene: gcvP Accession Numbers: EG11810 (EcoCyc), b2903, ECK2898

Synonyms: P-protein

Regulation Summary Diagram: ?

Component of: glycine cleavage system (extended summary available)

Subunit composition of glycine decarboxylase = [GcvP]2
         glycine decarboxylase = GcvP

Summary:
Together with GcvH, GcvT and E3 (Lpd), GvcP forms a loosely associated complex known as the glycine cleavage system. GvcP, also known as the P-protein, catalyzes the decarboxylation of glycine. The remaining aminomethyl moiety is transferred to the lipoyl prosthetic group of the H-protein [OkamuraIkeda93, Stauffer86].

Glycine cleavage system mutations cause a defect in utilization of glycine to form serine [Plamann83a]. Expression of the glycine cleavage enzyme system is induced by glycine [Meedel74, Stauffer94], and the transcriptional regulation of the gcvTHP operon has been studied extensively.

Review: [ECOSAL] Module 3.6.1.2

Gene Citations: [Zaslaver06]

Locations: cytosol

Map Position: [3,044,190 <- 3,047,063] (65.61 centisomes)
Length: 2874 bp / 957 aa

Molecular Weight of Polypeptide: 104.38 kD (from nucleotide sequence), 93.3 kD (experimental) [Stauffer93 ]

Molecular Weight of Multimer: 180 kD (experimental) [OkamuraIkeda93]

Unification Links: ASAP:ABE-0009531 , CGSC:28661 , DIP:DIP-9753N , EchoBASE:EB1758 , EcoGene:EG11810 , EcoliWiki:b2903 , Entrez-gene:947394 , Mint:MINT-1318484 , ModBase:P33195 , OU-Microarray:b2903 , PortEco:gcvP , PR:PRO_000022764 , Pride:P33195 , Protein Model Portal:P33195 , RefSeq:NP_417379 , RegulonDB:EG11810 , SMR:P33195 , String:511145.b2903 , UniProt:P33195

Relationship Links: InterPro:IN-FAMILY:IPR003437 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR020580 , InterPro:IN-FAMILY:IPR020581 , Panther:IN-FAMILY:PTHR11773 , Pfam:IN-FAMILY:PF02347

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006544 - glycine metabolic process Inferred by computational analysis [GOA01]
GO:0006546 - glycine catabolic process Inferred by computational analysis [GOA01]
GO:0019464 - glycine decarboxylation via glycine cleavage system Inferred by computational analysis [GOA06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0004375 - glycine dehydrogenase (decarboxylating) activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, OkamuraIkeda93]
GO:0042802 - identical protein binding Inferred from experiment [Lasserre06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0030170 - pyridoxal phosphate binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]

MultiFun Terms: metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis

Essentiality data for gcvP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 08-Feb-2007 by Keseler I , SRI International


Enzymatic reaction of: glycine decarboxylase

Synonyms: GcvP, glycine cleavage system P-protein, P-protein, glycine:lipoylprotein oxidoreductase (decarboxylationg and acceptor aminomethylating), glycine dehydrogenase (decarboxylating)

EC Number: 1.4.4.2

glycine + a [glycine-cleavage complex H protein] N6-lipoyl-L-lysine + H+ <=> a [glycine-cleavage complex H protein] N6-aminomethyldihydrolipoyl-L-lysine + CO2

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

In Pathways: glycine cleavage

Summary:
The presence of PLP as a prosthetic group appears to be inferred by similarity.

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate


Subunit of: glycine cleavage system

Subunit composition of glycine cleavage system = [(Lpd)2][(GcvP)2][GcvH][GcvT]
         lipoamide dehydrogenase = (Lpd)2 (extended summary available)
                 E3 monomer = Lpd
         glycine decarboxylase = (GcvP)2
                 glycine decarboxylase = GcvP
         lipoyl-GcvH-protein = GcvH
         aminomethyltransferase = GcvT (summary available)

Summary:
The glycine-cleavage system (GCV) is a multienzyme complex that catalyzes the reversible oxidation of glycine, yielding carbon dioxide, ammonia, 5,10-methylenetetrahydrofolate and a reduced pyridine nucleotide. Tetrahydrofolate serves as a recipient for one-carbon units generated during glycine cleavage to form the methylene group. The GCV system consists of four protein components, the P protein, H protein, T protein, and L protein. P protein catalyzes the pyridoxal phosphate-dependent liberation of CO2 from glycine, leaving a methylamine moiety. The methylamine moiety is transferred to the lipoic acid group of the H protein, which is bound to the P protein prior to decarboxylation of glycine. The T protein catalyzes the release of NH3 from the methylamine group and transfers the remaining C1 unit to THF, forming 5,10-mTHF. The L protein then oxidizes the lipoic acid component of the H protein and transfers the electrons to NAD+, forming NADH [OkamuraIkeda93].

Mutations that result in an enzymatic deficiency in the GCV enzyme system (gcvT, gcvH, and gcvP) do not result in auxotrophy. Mutations that result in an enzymatic deficiency in both the serine pathway and the GCV enzyme system can no longer use glycine as a serine source [Plamann83a].

Mutants that overproduce the GCV enzyme complex are partial glycine auxotrophs due to rapid glycine catabolism. [Ghrist95, Heil02].

One of the four subunits, lipoamide dehydrogenase (E3), is shared with pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase [Steiert90].

This topic has been reviewed in [Kikuchi08].

Credits:
Reviewed 04-Mar-2010 by Sarker M


Enzymatic reaction of: gcv system (glycine cleavage system)

Synonyms: glycine cleavage multienzyme system

glycine + a tetrahydrofolate + NAD+ <=> a 5,10-methylene-tetrahydrofolate + ammonium + CO2 + NADH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: glycine cleavage , N10-formyl-tetrahydrofolate biosynthesis

Summary:
This reaction represents the net reaction catalyzed by the glycine cleavage system enzyme complex.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
a 5,10-methylene-tetrahydrofolate
67.7
14.4
[OkamuraIkeda99, BRENDA14]
a 5,10-methylene-tetrahydrofolate
88.1
18.4
[OkamuraIkeda03, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[OkamuraIkeda93, UniProt11a]
UniProt: Removed.
Chain 2 -> 957
[UniProt09]
UniProt: Glycine dehydrogenase [decarboxylating];
N6-pyridoxal-phosphate-Lys-Modification 708
[UniProt11]
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2903 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11810; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Ghrist95: Ghrist AC, Stauffer GV (1995). "Characterization of the Escherichia coli gcvR gene encoding a negative regulator of gcv expression." J Bacteriol 177(17);4980-4. PMID: 7665475

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Heil02: Heil G, Stauffer LT, Stauffer GV (2002). "Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon." Microbiology 148(Pt 7);2203-14. PMID: 12101307

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kikuchi08: Kikuchi G, Motokawa Y, Yoshida T, Hiraga K (2008). "Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia." Proc Jpn Acad Ser B Phys Biol Sci 84(7);246-63. PMID: 18941301

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Meedel74: Meedel TH, Pizer LI (1974). "Regulation of one-carbon biosynthesis and utilization in Escherichia coli." J Bacteriol 118(3);905-10. PMID: 4598009

OkamuraIkeda03: Okamura-Ikeda K, Kameoka N, Fujiwara K, Motokawa Y (2003). "Probing the H-protein-induced conformational change and the function of the N-terminal region of Escherichia coli T-protein of the glycine cleavage system by limited proteolysis." J Biol Chem 278(12);10067-72. PMID: 12531904

OkamuraIkeda93: Okamura-Ikeda K, Ohmura Y, Fujiwara K, Motokawa Y (1993). "Cloning and nucleotide sequence of the gcv operon encoding the Escherichia coli glycine-cleavage system." Eur J Biochem 1993;216(2);539-48. PMID: 8375392

OkamuraIkeda99: Okamura-Ikeda K, Fujiwara K, Motokawa Y (1999). "Identification of the folate binding sites on the Escherichia coli T-protein of the glycine cleavage system." J Biol Chem 274(25);17471-7. PMID: 10364177

Plamann83a: Plamann MD, Rapp WD, Stauffer GV (1983). "Escherichia coli K12 mutants defective in the glycine cleavage enzyme system." Mol Gen Genet 192(1-2);15-20. PMID: 6358793

Stauffer86: Stauffer LT, Plamann MD, Stauffer GV (1986). "Cloning and characterization of the glycine-cleavage enzyme system of Escherichia coli." Gene 1986;44(2-3);219-26. PMID: 3023185

Stauffer93: Stauffer LT, Ghrist A, Stauffer GV (1993). "The Escherichia coli gcvT gene encoding the T-protein of the glycine cleavage enzyme system." DNA Seq 3(6);339-46. PMID: 8219277

Stauffer94: Stauffer LT, Fogarty SJ, Stauffer GV (1994). "Characterization of the Escherichia coli gcv operon." Gene 142(1);17-22. PMID: 8181752

Steiert90: Steiert PS, Stauffer LT, Stauffer GV (1990). "The lpd gene product functions as the L protein in the Escherichia coli glycine cleavage enzyme system." J Bacteriol 172(10);6142-4. PMID: 2211531

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

Other References Related to Gene Regulation

Cho11: Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BO (2011). "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res 39(15);6456-64. PMID: 21572102

Herrington13: Herrington MB, Sitaras C (2013). "The influence of CsgD on the expression of genes of folate metabolism and hmp in Escherichia coli K-12." Arch Microbiol 195(8);559-69. PMID: 23824318

Jourdan98: Jourdan AD, Stauffer GV (1998). "Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding." J Bacteriol 180(18);4865-71. PMID: 9733689

Jourdan99: Jourdan AD, Stauffer GV (1999). "Genetic analysis of the GcvA binding site in the gcvA control region." Microbiology 145 ( Pt 8);2153-62. PMID: 10463182

McArthur06: McArthur SD, Pulvermacher SC, Stauffer GV (2006). "The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules." BMC Microbiol 6;52. PMID: 16768793

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

Stauffer05: Stauffer LT, Stauffer GV (2005). "GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon." FEMS Microbiol Lett 242(2);333-8. PMID: 15621456

Stauffer94a: Stauffer LT, Stauffer GV (1994). "Characterization of the gcv control region from Escherichia coli." J Bacteriol 176(20);6159-64. PMID: 7928983

Stauffer98: Stauffer LT, Stauffer GV (1998). "Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli." Microbiology 144 ( Pt 5);1417-22. PMID: 9611815

Stauffer98a: Stauffer LT, Stauffer GV (1998). "Roles for GcvA-binding sites 3 and 2 and the Lrp-binding region in gcvT::lacZ expression in Escherichia coli." Microbiology 144 ( Pt 10);2865-72. PMID: 9802028

Stauffer99: Stauffer LT, Stauffer GV (1999). "Role for the leucine-responsive regulatory protein (Lrp) as a structural protein in regulating the Escherichia coli gcvTHP operon." Microbiology 145 ( Pt 3);569-76. PMID: 10217490

Wilson93: Wilson RL, Steiert PS, Stauffer GV (1993). "Positive regulation of the Escherichia coli glycine cleavage enzyme system." J Bacteriol 175(3);902-4. PMID: 8423160

Wilson94: Wilson RL, Stauffer GV (1994). "DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system." J Bacteriol 176(10);2862-8. PMID: 8188587

Wilson95: Wilson RL, Urbanowski ML, Stauffer GV (1995). "DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli." J Bacteriol 177(17);4940-6. PMID: 7665470

Wonderling00: Wonderling LD, Urbanowski ML, Stauffer GV (2000). "GcvA binding site 1 in the gcvTHP promoter of Escherichia coli is required for GcvA-mediated repression but not for GcvA-mediated activation." Microbiology 146 ( Pt 11);2909-18. PMID: 11065369

Wonderling99: Wonderling LD, Stauffer GV (1999). "The cyclic AMP receptor protein is dependent on GcvA for regulation of the gcv operon." J Bacteriol 181(6);1912-9. PMID: 10074087


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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