RegulonDB

Gene
Name:	serA
Synonym(s):	ECK2909, EG10944, b2913
Genome position(nucleotides):	3057178 <-- 3058410 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.96
External database links:

ASAP:	ABE-0009561
CGSC:	173
ECHOBASE:	EB0937
MIM:	256520
MIM:	601815
OU-MICROARRAY:	b2913
PortEco:	serA
STRING:	511145.b2913
COLOMBOS:	serA

Gene

Name:

serA

Synonym(s):

ECK2909, EG10944, b2913

Genome position(nucleotides):

3057178 <-- 3058410 Genome Browser

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.96

External database links:

ASAP:

CGSC:

ECHOBASE:

MIM:

MIM:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

238 -> 240

ASR

292 -> 295

HIGG

345 -> 401

ENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIP

2 -> 410

AKVSLEKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY

14 -> 326

LLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGCFCIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVN

Type

Positions

Sequence

238 -> 240

ASR

292 -> 295

HIGG

345 -> 401

ENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIP

2 -> 410

14 -> 326

118 -> 294

GELLLLLRGVPEANAKAHRGVWNKLAAGSFEARGKKLGIIGYGHIGTQLGILAESLGMYVYFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENPSTKNMMGAKEISLMKPGSLLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVLLTPHIG

161 -> 162

339 -> 410

RLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDIEADEDVAEKALQAMKAIPGTIRARLLY

Multifun Terms (GenProtEC)

1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.1 - amino acids --> 1.5.1.11 - serine

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol

molecular_function

GO:0016491 - oxidoreductase activity
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0004617 - phosphoglycerate dehydrogenase activity
GO:0047545 - 2-hydroxyglutarate dehydrogenase activity
GO:0030267 - glyoxylate reductase (NADP) activity
GO:0042802 - identical protein binding
GO:0051287 - NAD binding
GO:0016618 - hydroxypyruvate reductase activity
GO:0070403 - NAD+ binding
GO:0070905 - serine binding
GO:0070404 - NADH binding

biological_process

GO:0006564 - L-serine biosynthetic process
GO:0008652 - cellular amino acid biosynthetic process
GO:0055114 - oxidation-reduction process

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, Lrp
Repressed by:	Nac, Lrp

Transcriptional Regulation

Display Regulation

Activated by:

CRP, Lrp

Repressed by:

Nac, Lrp

Regulation by small RNA
	Display Regulation
small RNA	gcvB

Regulation by small RNA

Display Regulation

small RNA

gcvB

Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
srna	SibC	3056890	3056949	reverse	unknow.	nd	nd
promoter	TSS_3193	3057340		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3194	3057467		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3195	3057593		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3196	3057726		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3197	3057734		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3198	3058242		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3199	3058303		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3200	3058379		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3201	3058419		reverse	nd	[RS-EPT-CBR]	[7]
promoter	TSS_3202 (cluster)	3058434		reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 3058433 to 3058434, where the highest frequency is at position 3056455. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[7]
promoter	TSS_3203	3058455		reverse	nd	[RS-EPT-CBR]	[7]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

srna

SibC

3056890

3056949

reverse

unknow.

promoter

TSS_3193

3057340

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3194

3057467

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3195

3057593

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3196

3057726

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3197

3057734

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3198

3058242

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3199

3058303

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3200

3058379

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3201

3058419

reverse

[RS-EPT-CBR]

[7]

promoter

TSS_3202 (cluster)

3058434

reverse

For this promoter, there
Read more >

[RS-EPT-CBR]

[7]

promoter

TSS_3203

3058455

reverse

[RS-EPT-CBR]

[7]

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] Burton RL., Chen S., Xu XL., Grant GA., 2009, Transient kinetic analysis of the interaction of L-serine with Escherichia coli D-3-phosphoglycerate dehydrogenase reveals the mechanism of V-type regulation and the order of effector binding., Biochemistry 48(51):12242-51
[2] Deng H., Chen C., Sun C., Wei C., 2016, [Construction and characterization of Escherichia coli D-3-phosphoglycerate dehydrogenase mutants with feedback-inhibition relief]., Sheng Wu Gong Cheng Xue Bao 32(4):468-477
[3] Kim HJ., Hou BK., Lee SG., Kim JS., Lee DW., Lee SJ., 2013, Genome-wide analysis of redox reactions reveals metabolic engineering targets for D-lactate overproduction in Escherichia coli., Metab Eng 18:44-52
[4] Li Y., Chen GK., Tong XW., Zhang HT., Liu XG., Liu YH., Lu FP., 2012, Construction of Escherichia coli strains producing L-serine from glucose., Biotechnol Lett 34(8):1525-30
[5] Mundhada H., Schneider K., Christensen HB., Nielsen AT., 2016, Engineering of high yield production of L-serine in Escherichia coli., Biotechnol Bioeng 113(4):807-16
[6] Tobey KL., Grant GA., 1986, The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase., J Biol Chem 261(26):12179-83
[7] 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] Burton RL., Chen S., Xu XL., Grant GA., 2009, Transient kinetic analysis of the interaction of L-serine with Escherichia coli D-3-phosphoglycerate dehydrogenase reveals the mechanism of V-type regulation and the order of effector binding., Biochemistry 48(51):12242-51

[2] Deng H., Chen C., Sun C., Wei C., 2016, [Construction and characterization of Escherichia coli D-3-phosphoglycerate dehydrogenase mutants with feedback-inhibition relief]., Sheng Wu Gong Cheng Xue Bao 32(4):468-477

[3] Kim HJ., Hou BK., Lee SG., Kim JS., Lee DW., Lee SJ., 2013, Genome-wide analysis of redox reactions reveals metabolic engineering targets for D-lactate overproduction in Escherichia coli., Metab Eng 18:44-52

[4] Li Y., Chen GK., Tong XW., Zhang HT., Liu XG., Liu YH., Lu FP., 2012, Construction of Escherichia coli strains producing L-serine from glucose., Biotechnol Lett 34(8):1525-30

[5] Mundhada H., Schneider K., Christensen HB., Nielsen AT., 2016, Engineering of high yield production of L-serine in Escherichia coli., Biotechnol Bioeng 113(4):807-16

[6] Tobey KL., Grant GA., 1986, The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase., J Biol Chem 261(26):12179-83

[7] 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.