RegulonDB

Gene
Name:	glyA
Synonym(s):	ECK2548, EG10408, b2551
Genome position(nucleotides):	2684254 <-- 2685507
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.35
External database links:

ASAP:	ABE-0008389
CGSC:	675
ECHOBASE:	EB0403
ECOLIHUB:	glyA
NCBI-GENE:	947022
OU-MICROARRAY:	b2551
STRING:	511145.b2551
COLOMBOS:	glyA

Gene

Name:

glyA

Synonym(s):

ECK2548, EG10408, b2551

Genome position(nucleotides):

2684254 <-- 2685507

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

53.35

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

NCBI-GENE:

OU-MICROARRAY:

STRING:

COLOMBOS:

Shine dalgarno
Sequence:	ttagctgagtCAGGAGatgcgGAT

Shine dalgarno

Sequence:

ttagctgagtCAGGAGatgcgGAT

Type

Positions

Sequence

Comment

9 -> 386

ADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDATGHIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVEVFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWM

55 -> 55

UniProt: 50 and 15-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 4-fold decrease in the catalytic efficiency..

65 -> 65

UniProt: Decrease in catalytic activity..

85 -> 85

UniProt: Alteration of the dimer-monomer equilibrium accompanied by minor changes in the catalytic properties and whitout any significant change of tertiary structure. In the monomeric state; when associated with A-276..

125 -> 127

GHL

UniProt: Substrate binding; Sequence Annotation Type: region of interest.

Type

Positions

Sequence

Comment

9 -> 386

55 -> 55

UniProt: 50 and 15-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 4-fold decrease in the catalytic efficiency..

65 -> 65

UniProt: Decrease in catalytic activity..

85 -> 85

125 -> 127

GHL

UniProt: Substrate binding; Sequence Annotation Type: region of interest.

214 -> 214

UniProt: No significant difference in catalytic efficiency and affinity compared to the wild-type..

216 -> 216

UniProt: Important decrease in affinity and catalytic efficiency. Severely compromised in folding into a catalytically competent enzyme..

218 -> 218

UniProt: No significant difference in catalytic efficiency and affinity compared to the wild-type..

235 -> 235

UniProt: 900- and 17-fold increase in the affinity for serine and tetrahydrofolate, respectively, and 30-fold decrease in the catalytic efficiency..

258 -> 258

UniProt: Important decrease in affinity and catalytic efficiency..

264 -> 264

UniProt: Important decrease in affinity and catalytic efficiency..

276 -> 276

355 -> 357

SPF

UniProt: Substrate binding; Sequence Annotation Type: region of interest.

363 -> 363

UniProt: Exhibits only 0.03% of the catalytic activity of the wild-type and a 15-fold reduction in affinity for glycine and serine..

372 -> 372

UniProt: No significant difference compared to the wild-type..

Multifun Terms (GenProtEC)

1 - metabolism --> 1.1 - carbon utilization --> 1.1.3 - amino acids

1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.1 - amino acids --> 1.5.1.10 - glycine

1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.17 - formyl-THF biosynthesis

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane

molecular_function

GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0030170 - pyridoxal phosphate binding
GO:0004372 - glycine hydroxymethyltransferase activity
GO:0008270 - zinc ion binding
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0070905 - serine binding

biological_process

GO:0006545 - glycine biosynthetic process
GO:0006564 - L-serine biosynthetic process
GO:0006730 - one-carbon metabolic process
GO:0008652 - cellular amino acid biosynthetic process
GO:0046655 - folic acid metabolic process
GO:0006546 - glycine catabolic process
GO:0006565 - L-serine catabolic process
GO:0019264 - glycine biosynthetic process from serine
GO:0046653 - tetrahydrofolate metabolic process
GO:0035999 - tetrahydrofolate interconversion

Transcriptional Regulation
	Display Regulation
Activated by:	MetR
Repressed by:	MetR, PurR

Transcriptional Regulation

Display Regulation

Activated by:

MetR

Repressed by:

MetR, PurR

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_2836 (cluster)	2684844	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2837	2684848	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2838	2684852	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2839	2684858	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2840	2684978	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2841	2685334	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2842	2685346	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2843	2685533	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2844 (cluster)	2685538	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_2845 (cluster)	2685572	reverse	nd	[RS-EPT-CBR]	[5]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_2836 (cluster)

2684844

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2837

2684848

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2838

2684852

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2839

2684858

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2840

2684978

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2841

2685334

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2842

2685346

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2843

2685533

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2844 (cluster)

2685538

reverse

[RS-EPT-CBR]

[5]

promoter

TSS_2845 (cluster)

2685572

reverse

[RS-EPT-CBR]

[5]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Blank D., Wolf L., Ackermann M., Silander OK., 2014, The predictability of molecular evolution during functional innovation., Proc Natl Acad Sci U S A 111(8):3044-9
[2] 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
[3] Loscha KV., Otting G., 2013, Biosynthetically directed ²H labelling for stereospecific resonance assignments of glycine methylene groups., J Biomol NMR 55(1):97-104
[4] Shen T., Rui B., Zhou H., Zhang X., Yi Y., Wen H., Zheng H., Wu J., Shi Y., 2013, Metabolic flux ratio analysis and multi-objective optimization revealed a globally conserved and coordinated metabolic response of E. coli to paraquat-induced oxidative stress., Mol Biosyst 9(1):121-32
[5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Blank D., Wolf L., Ackermann M., Silander OK., 2014, The predictability of molecular evolution during functional innovation., Proc Natl Acad Sci U S A 111(8):3044-9

[2] 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

[3] Loscha KV., Otting G., 2013, Biosynthetically directed ²H labelling for stereospecific resonance assignments of glycine methylene groups., J Biomol NMR 55(1):97-104

[4] Shen T., Rui B., Zhou H., Zhang X., Yi Y., Wen H., Zheng H., Wu J., Shi Y., 2013, Metabolic flux ratio analysis and multi-objective optimization revealed a globally conserved and coordinated metabolic response of E. coli to paraquat-induced oxidative stress., Mol Biosyst 9(1):121-32

[5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.