RegulonDB

Gene
Name:	alaS
Synonym(s):	ECK2692, EG10034, act, ala-act, b2697, lovB
Genome position(nucleotides):	2819381 <-- 2822011
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.63
External database links:

ASAP:	ABE-0008869
CGSC:	1039
ECHOBASE:	EB0033
ECOLIHUB:	alaS
MIM:	613287
MIM:	616339
OU-MICROARRAY:	b2697
STRING:	511145.b2697
COLOMBOS:	alaS

Gene

Name:

alaS

Synonym(s):

ECK2692, EG10034, act, ala-act, b2697, lovB

Genome position(nucleotides):

2819381 <-- 2822011

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

53.63

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

MIM:

MIM:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

2 -> 876

SKSTAEIRQAFLDFFHSKGHQVVASSSLVPHNDPTLLFTNAGMNQFKDVFLGLDKRNYSRATTSQRCVRAGGKHNDLENVGYTARHHTFFEMLGNFSFGDYFKHDAIQFAWELLTSEKWFALPKERLWVTVYESDDEAYEIWEKEVGIPRERIIRIGDNKGAPYASDNFWQMGDTGPCGPCTEIFYDHGDHIWGGPPGSPEEDGDRYIEIWNIVFMQFNRQADGTMEPLPKPSVDTGMGLERIAAVLQHVNSNYDIDLFRTLIQAVAKVTGATDLSNKSLRVIADHIRSCAFLIADGVMPSNENRGYVLRRIIRRAVRHGNMLGAKETFFYKLVGPLIDVMGSAGEDLKRQQAQVEQVLKTEEEQFARTLERGLALLDEELAKLSGDTLDGETAFRLYDTYGFPVDLTADVCRERNIKVDEAGFEAAMEEQRRRAREASGFGADYNAMIRVDSASEFKGYDHLELNGKVTALFVDGKAVDAINAGQEAVVVLDQTPFYAESGGQVGDKGELKGANFSFAVEDTQKYGQAIGHIGKLAAGSLKVGDAVQADVDEARRARIRLNHSATHLMHAALRQVLGTHVSQKGSLVNDKVLRFDFSHNEAMKPEEIRAVEDLVNTQIRRNLPIETNIMDLEAAKAKGAMALFGEKYDERVRVLSMGDFSTELCGGTHASRTGDIGLFRIISESGTAAGVRRIEAVTGEGAIATVHADSDRLSEVAHLLKGDSNNLADKVRSVLERTRQLEKELQQLKEQAAAQESANLSSKAIDVNGVKLLVSELSGVEPKMLRTMVDDLKNQLGSTIIVLATVVEGKVSLIAGVSKDVTDRVKAGELIGMVAQQVGGKGGGRPDMAQAGGTDAAALPAALASVKGWVSAKLQ

UniProt: Alanine--tRNA ligase.

7 -> 556

EIRQAFLDFFHSKGHQVVASSSLVPHNDPTLLFTNAGMNQFKDVFLGLDKRNYSRATTSQRCVRAGGKHNDLENVGYTARHHTFFEMLGNFSFGDYFKHDAIQFAWELLTSEKWFALPKERLWVTVYESDDEAYEIWEKEVGIPRERIIRIGDNKGAPYASDNFWQMGDTGPCGPCTEIFYDHGDHIWGGPPGSPEEDGDRYIEIWNIVFMQFNRQADGTMEPLPKPSVDTGMGLERIAAVLQHVNSNYDIDLFRTLIQAVAKVTGATDLSNKSLRVIADHIRSCAFLIADGVMPSNENRGYVLRRIIRRAVRHGNMLGAKETFFYKLVGPLIDVMGSAGEDLKRQQAQVEQVLKTEEEQFARTLERGLALLDEELAKLSGDTLDGETAFRLYDTYGFPVDLTADVCRERNIKVDEAGFEAAMEEQRRRAREASGFGADYNAMIRVDSASEFKGYDHLELNGKVTALFVDGKAVDAINAGQEAVVVLDQTPFYAESGGQVGDKGELKGANFSFAVEDTQKYGQAIGHIGKLAAGSLKVGDAVQADVDEAR

29 -> 33

LVPHN

UniProt: In Ref. 4; no nucleotide entry and 5; AAA03208..

158 -> 158

UniProt: In Ref. 4; no nucleotide entry and 5; AAA03208..

168 -> 168

UniProt: In Ref. 5; AAA03208..

Type

Positions

Sequence

Comment

2 -> 876

UniProt: Alanine--tRNA ligase.

7 -> 556

29 -> 33

LVPHN

UniProt: In Ref. 4; no nucleotide entry and 5; AAA03208..

158 -> 158

UniProt: In Ref. 4; no nucleotide entry and 5; AAA03208..

168 -> 168

UniProt: In Ref. 5; AAA03208..

172 -> 172

UniProt: In Ref. 5; AAA03208..

175 -> 175

UniProt: In Ref. 5; AAA03208..

179 -> 179

UniProt: Inactivates the enzyme..

180 -> 180

UniProt: In Ref. 5; AAA03208..

182 -> 182

UniProt: No inactivation..

184 -> 184

UniProt: No inactivation..

188 -> 188

UniProt: No inactivation..

189 -> 189

UniProt: Inactivates the enzyme..

191 -> 191

UniProt: No inactivation..

192 -> 192

UniProt: Inactivates the enzyme..

236 -> 236

UniProt: Decreases affinity for alanine without improving discrimination against serine..

238 -> 238

UniProt: Greatly decreases affinity for alanine with only small changes in affinity for serine and glycine, in a 2-442 residue construct..

553 -> 705

DEARRARIRLNHSATHLMHAALRQVLGTHVSQKGSLVNDKVLRFDFSHNEAMKPEEIRAVEDLVNTQIRRNLPIETNIMDLEAAKAKGAMALFGEKYDERVRVLSMGDFSTELCGGTHASRTGDIGLFRIISESGTAAGVRRIEAVTGEGAIA

UniProt: Editing; Sequence Annotation Type: region of interest.

564 -> 564

UniProt: No effect on tRNA editing..

567 -> 567

UniProt: Complete loss of tRNA editing; when associated with W-587 and F-666..

568 -> 568

UniProt: No effect on tRNA editing..

584 -> 584

UniProt: In Ref. 5; AAA03208..

587 -> 587

UniProt: Complete loss of tRNA editing; when associated with F-567 and F-666..

619 -> 619

UniProt: In Ref. 5; AAA03208..

653 -> 696

VRVLSMGDFSTELCGGTHASRTGDIGLFRIISESGTAAGVRRIE

666 -> 666

UniProt: Loss of mischarged tRNA editing activity; when associated with H-584 the effect is more pronounced..

670 -> 670

UniProt: No effect on tRNA editing..

693 -> 693

UniProt: Reduces specificity of editing activity for tRNA(Ala), allows editing of tRNA(Thr)..

699 -> 808

TGEGAIATVHADSDRLSEVAHLLKGDSNNLADKVRSVLERTRQLEKELQQLKEQAAAQESANLSSKAIDVNGVKLLVSELSGVEPKMLRTMVDDLKNQLGSTIIVLATVV

UniProt: Important for oligomerization; Sequence Annotation Type: region of interest.

732 -> 871

VRSVLERTRQLEKELQQLKEQAAAQESANLSSKAIDVNGVKLLVSELSGVEPKMLRTMVDDLKNQLGSTIIVLATVVEGKVSLIAGVSKDVTDRVKAGELIGMVAQQVGGKGGGRPDMAQAGGTDAAALPAALASVKGWV

766 -> 875

IDVNGVKLLVSELSGVEPKMLRTMVDDLKNQLGSTIIVLATVVEGKVSLIAGVSKDVTDRVKAGELIGMVAQQVGGKGGGRPDMAQAGGTDAAALPAALASVKGWVSAKL

UniProt: C-Ala domain; Sequence Annotation Type: region of interest.

Multifun Terms (GenProtEC)

2 - information transfer --> 2.3 - protein related --> 2.3.1 - amino acid -activation

3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor

Gene Ontology Terms (GO)

cellular_component

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

molecular_function

GO:0003676 - nucleic acid binding
GO:0046872 - metal ion binding
GO:0016874 - ligase activity
GO:0004812 - aminoacyl-tRNA ligase activity
GO:0004813 - alanine-tRNA ligase activity
GO:0003723 - RNA binding
GO:0000049 - tRNA binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0016597 - amino acid binding
GO:0008270 - zinc ion binding
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0002161 - aminoacyl-tRNA editing activity
GO:0001217 - DNA-binding transcription repressor activity
GO:0002196 - Ser-tRNA(Ala) hydrolase activity

biological_process

GO:0106074 - aminoacyl-tRNA metabolism involved in translational fidelity
GO:0006400 - tRNA modification
GO:0006412 - translation
GO:0043039 - tRNA aminoacylation
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0006419 - alanyl-tRNA aminoacylation

Transcriptional Regulation
	Display Regulation
Repressed by:	AlaS

Transcriptional Regulation

Display Regulation

Repressed by:

AlaS

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_3006	2819585	reverse	nd	[RS-EPT-CBR]	[6]
promoter	TSS_3007 (cluster)	2819687	reverse	nd	[RS-EPT-CBR]	[6]
promoter	TSS_3008	2821435	reverse	nd	[RS-EPT-CBR]	[6]
promoter	TSS_3009	2822024	reverse	nd	[RS-EPT-CBR]	[6]
promoter	TSS_3010	2822039	reverse	nd	[RS-EPT-CBR]	[6]
promoter	TSS_3011	2822087	reverse	nd	[RS-EPT-CBR]	[6]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_3006

2819585

reverse

[RS-EPT-CBR]

[6]

promoter

TSS_3007 (cluster)

2819687

reverse

[RS-EPT-CBR]

[6]

promoter

TSS_3008

2821435

reverse

[RS-EPT-CBR]

[6]

promoter

TSS_3009

2822024

reverse

[RS-EPT-CBR]

[6]

promoter

TSS_3010

2822039

reverse

[RS-EPT-CBR]

[6]

promoter

TSS_3011

2822087

reverse

[RS-EPT-CBR]

[6]

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] Banerjee B., Banerjee R., 2014, Guanidine hydrochloride mediated denaturation of E. coli Alanyl-tRNA synthetase: identification of an inactive dimeric intermediate., Protein J 33(2):119-27
[2] Guo M., Shapiro R., Schimmel P., Yang XL., 2010, Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase., Acta Crystallogr D Biol Crystallogr 66(Pt 3):243-50
[3] Liu Z., Vargas-Rodriguez O., Goto Y., Novoa EM., Ribas de Pouplana L., Suga H., Musier-Forsyth K., 2015, Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation., Proc Natl Acad Sci U S A 112(19):6027-32
[4] Sun L., Gomes AC., He W., Zhou H., Wang X., Pan DW., Schimmel P., Pan T., Yang XL., 2016, Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair., J Am Chem Soc 138(39):12948-12955
[5] Yao P., Poruri K., Martinis SA., Fox PL., 2014, Non-catalytic regulation of gene expression by aminoacyl-tRNA synthetases., Top Curr Chem 344:167-87
[6] 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] Banerjee B., Banerjee R., 2014, Guanidine hydrochloride mediated denaturation of E. coli Alanyl-tRNA synthetase: identification of an inactive dimeric intermediate., Protein J 33(2):119-27

[2] Guo M., Shapiro R., Schimmel P., Yang XL., 2010, Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase., Acta Crystallogr D Biol Crystallogr 66(Pt 3):243-50

[3] Liu Z., Vargas-Rodriguez O., Goto Y., Novoa EM., Ribas de Pouplana L., Suga H., Musier-Forsyth K., 2015, Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation., Proc Natl Acad Sci U S A 112(19):6027-32

[4] Sun L., Gomes AC., He W., Zhou H., Wang X., Pan DW., Schimmel P., Pan T., Yang XL., 2016, Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair., J Am Chem Soc 138(39):12948-12955

[5] Yao P., Poruri K., Martinis SA., Fox PL., 2014, Non-catalytic regulation of gene expression by aminoacyl-tRNA synthetases., Top Curr Chem 344:167-87

[6] 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.