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Protein

Alanine--tRNA ligase

Gene

alaS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). AlaRS also incorrectly activates the sterically smaller than alanine amino acid glycine as well as the sterically larger amino acid serine. These incorrectly charged amino acids occur because the of inherent physicochemical limitations on discrimination between closely related amino acids (glycine and serine) in the charging step.
Edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) but not incorrectly charged Ser-tRNA(Thr).
Attaches Ala to transfer-messenger RNA (tmRNA, also known as 10Sa RNA, the product of the ssrA gene). tmRNA plays a major role in rescue of stalled ribosomes via trans-translation.1 Publication

Catalytic activityi

ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala).

Cofactori

Zn2+Note: Binds 1 zinc ion per subunit; it is not clear where this binding occurs.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi564ZincBy similarity1
Metal bindingi568ZincBy similarity1
Metal bindingi666ZincBy similarity1
Metal bindingi670ZincBy similarity1

GO - Molecular functioni

  • alanine-tRNA ligase activity Source: EcoCyc
  • amino acid binding Source: GO_Central
  • aminoacyl-tRNA editing activity Source: UniProtKB
  • ATP binding Source: UniProtKB-HAMAP
  • transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding Source: EcoCyc
  • tRNA binding Source: GO_Central
  • zinc ion binding Source: EcoCyc

GO - Biological processi

  • alanyl-tRNA aminoacylation Source: EcoCyc
  • negative regulation of transcription, DNA-templated Source: EcoCyc
  • tRNA modification Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, RNA-binding, tRNA-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:ALAS-MONOMER.
ECOL316407:JW2667-MONOMER.
MetaCyc:ALAS-MONOMER.
BRENDAi6.1.1.7. 2026.

Protein family/group databases

MoonProtiP00957.

Names & Taxonomyi

Protein namesi
Recommended name:
Alanine--tRNA ligase (EC:6.1.1.7)
Alternative name(s):
Alanyl-tRNA synthetase
Short name:
AlaRS
Gene namesi
Name:alaS
Synonyms:lovB
Ordered Locus Names:b2697, JW2667
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10034. alaS.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi179C → S: Inactivates the enzyme. 1 Publication1
Mutagenesisi182C → S: No inactivation. 1 Publication1
Mutagenesisi184E → Q: No inactivation. 1 Publication1
Mutagenesisi188D → N: No inactivation. 1 Publication1
Mutagenesisi189H → Q: Inactivates the enzyme. 1 Publication1
Mutagenesisi191D → N: No inactivation. 1 Publication1
Mutagenesisi192H → Q: Inactivates the enzyme. 1 Publication1
Mutagenesisi236D → A or N: Decreases affinity for alanine without improving discrimination against serine. 1 Publication1
Mutagenesisi238G → A: Greatly decreases affinity for alanine with only small changes in affinity for serine and glycine, in a 2-442 residue construct. 1 Publication1
Mutagenesisi564H → A: No effect on tRNA editing. 1 Publication1
Mutagenesisi568H → A: No effect on tRNA editing. 1 Publication1
Mutagenesisi584Q → H: Loss of mischarged tRNA editing activity; when associated with A-666. 2 Publications1
Mutagenesisi666C → A: Loss of mischarged tRNA editing activity; when associated with H-584 the effect is more pronounced. 2 Publications1
Mutagenesisi670H → A: No effect on tRNA editing. 1 Publication1
Mutagenesisi693R → K: Reduces specificity of editing activity for tRNA(Ala), allows editing of tRNA(Thr). 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000751132 – 876Alanine--tRNA ligaseAdd BLAST875

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei74N6-acetyllysine1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP00957.
PaxDbiP00957.
PRIDEiP00957.

2D gel databases

SWISS-2DPAGEP00957.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-544061,EBI-544061

Protein-protein interaction databases

BioGridi851507. 1 interactor.
DIPiDIP-9080N.
IntActiP00957. 19 interactors.
MINTiMINT-1266342.
STRINGi511145.b2697.

Structurei

Secondary structure

1876
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi5 – 18Combined sources14
Helixi43 – 47Combined sources5
Helixi48 – 51Combined sources4
Beta strandi60 – 69Combined sources10
Helixi78 – 80Combined sources3
Turni81 – 83Combined sources3
Beta strandi84 – 86Combined sources3
Beta strandi89 – 101Combined sources13
Helixi104 – 116Combined sources13
Turni118 – 121Combined sources4
Helixi125 – 127Combined sources3
Beta strandi128 – 133Combined sources6
Helixi137 – 145Combined sources9
Helixi151 – 153Combined sources3
Beta strandi154 – 157Combined sources4
Beta strandi170 – 188Combined sources19
Turni201 – 204Combined sources4
Beta strandi205 – 221Combined sources17
Beta strandi223 – 225Combined sources3
Beta strandi227 – 240Combined sources14
Helixi241 – 248Combined sources8
Helixi254 – 256Combined sources3
Helixi258 – 271Combined sources14
Helixi279 – 296Combined sources18
Helixi305 – 324Combined sources20
Helixi331 – 334Combined sources4
Helixi335 – 342Combined sources8
Helixi343 – 346Combined sources4
Helixi347 – 351Combined sources5
Helixi353 – 368Combined sources16
Helixi371 – 383Combined sources13
Beta strandi387 – 390Combined sources4
Helixi392 – 402Combined sources11
Helixi406 – 414Combined sources9
Turni415 – 417Combined sources3
Helixi422 – 440Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3HXUX-ray2.10A2-442[»]
3HXVX-ray1.93A2-442[»]
3HXWX-ray1.93A2-442[»]
3HXXX-ray2.11A2-442[»]
3HXYX-ray2.27A2-442[»]
3HXZX-ray1.99A/B/C/D2-442[»]
3HY0X-ray1.90A/B2-442[»]
3HY1X-ray2.79A/B2-442[»]
ProteinModelPortaliP00957.
SMRiP00957.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00957.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 461CatalyticAdd BLAST460
Regioni553 – 705EditingAdd BLAST153
Regioni699 – 808Important for oligomerizationAdd BLAST110
Regioni766 – 875C-Ala domainAdd BLAST110

Domaini

Consists of three domains; the N-terminal catalytic domain, the editing domain and the C-terminal C-Ala domain. The editing domain removes incorrectly charged amino acids, while the C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs.
The editing domain removes incorrectly charged amino acids, i.e. Ser-tRNA(Ala) or Gly-tRNA(Ala) become uncharged tRNA(Ala) and the amino acid. It is specific for the acceptor stem of tRNA(Ala).
The C-terminal C-Ala domain, along with tRNA(Ala), serves as a bridge to cooperatively bring together the editing and aminoacylation centers thus stimulating deacylation of misacylated tRNAs. This C-Ala domain can be replaced in vitro by the corresponding domain of Aquifex aeolicus or man. Recognition of tRNA(Ala) by the 2 domains is independent, that is one enzyme recognizes the same tRNA(Ala) in 2 different manners.Curated

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CIM. Bacteria.
COG0013. LUCA.
HOGENOMiHOG000156964.
InParanoidiP00957.
KOiK01872.
OMAiFDFNCPR.
PhylomeDBiP00957.

Family and domain databases

HAMAPiMF_00036_B. Ala_tRNA_synth_B. 1 hit.
InterProiIPR002318. Ala-tRNA-lgiase_IIc.
IPR018162. Ala-tRNA-ligase_IIc_anticod-bd.
IPR018165. Ala-tRNA-synth_IIc_core.
IPR018164. Ala-tRNA-synth_IIc_N.
IPR023033. Ala_tRNA_ligase_euk/bac.
IPR003156. DHHA1_dom.
IPR018163. Thr/Ala-tRNA-synth_IIc_edit.
IPR009000. Transl_B-barrel.
IPR012947. tRNA_SAD.
[Graphical view]
PfamiPF02272. DHHA1. 1 hit.
PF01411. tRNA-synt_2c. 1 hit.
PF07973. tRNA_SAD. 1 hit.
[Graphical view]
PRINTSiPR00980. TRNASYNTHALA.
SMARTiSM00863. tRNA_SAD. 1 hit.
[Graphical view]
SUPFAMiSSF101353. SSF101353. 1 hit.
SSF50447. SSF50447. 1 hit.
SSF55186. SSF55186. 1 hit.
TIGRFAMsiTIGR00344. alaS. 1 hit.
PROSITEiPS50860. AA_TRNA_LIGASE_II_ALA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P00957-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKSTAEIRQ AFLDFFHSKG HQVVASSSLV PHNDPTLLFT NAGMNQFKDV
60 70 80 90 100
FLGLDKRNYS RATTSQRCVR AGGKHNDLEN VGYTARHHTF FEMLGNFSFG
110 120 130 140 150
DYFKHDAIQF AWELLTSEKW FALPKERLWV TVYESDDEAY EIWEKEVGIP
160 170 180 190 200
RERIIRIGDN KGAPYASDNF WQMGDTGPCG PCTEIFYDHG DHIWGGPPGS
210 220 230 240 250
PEEDGDRYIE IWNIVFMQFN RQADGTMEPL PKPSVDTGMG LERIAAVLQH
260 270 280 290 300
VNSNYDIDLF RTLIQAVAKV TGATDLSNKS LRVIADHIRS CAFLIADGVM
310 320 330 340 350
PSNENRGYVL RRIIRRAVRH GNMLGAKETF FYKLVGPLID VMGSAGEDLK
360 370 380 390 400
RQQAQVEQVL KTEEEQFART LERGLALLDE ELAKLSGDTL DGETAFRLYD
410 420 430 440 450
TYGFPVDLTA DVCRERNIKV DEAGFEAAME EQRRRAREAS GFGADYNAMI
460 470 480 490 500
RVDSASEFKG YDHLELNGKV TALFVDGKAV DAINAGQEAV VVLDQTPFYA
510 520 530 540 550
ESGGQVGDKG ELKGANFSFA VEDTQKYGQA IGHIGKLAAG SLKVGDAVQA
560 570 580 590 600
DVDEARRARI RLNHSATHLM HAALRQVLGT HVSQKGSLVN DKVLRFDFSH
610 620 630 640 650
NEAMKPEEIR AVEDLVNTQI RRNLPIETNI MDLEAAKAKG AMALFGEKYD
660 670 680 690 700
ERVRVLSMGD FSTELCGGTH ASRTGDIGLF RIISESGTAA GVRRIEAVTG
710 720 730 740 750
EGAIATVHAD SDRLSEVAHL LKGDSNNLAD KVRSVLERTR QLEKELQQLK
760 770 780 790 800
EQAAAQESAN LSSKAIDVNG VKLLVSELSG VEPKMLRTMV DDLKNQLGST
810 820 830 840 850
IIVLATVVEG KVSLIAGVSK DVTDRVKAGE LIGMVAQQVG GKGGGRPDMA
860 870
QAGGTDAAAL PAALASVKGW VSAKLQ
Length:876
Mass (Da):96,032
Last modified:November 1, 1997 - v2
Checksum:i73F69C69FCF8C08C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti29 – 33LVPHN → RYPIT (PubMed:7005898).Curated5
Sequence conflicti29 – 33LVPHN → RYPIT in AAA03208 (PubMed:7025207).Curated5
Sequence conflicti158G → N (PubMed:7005898).Curated1
Sequence conflicti158G → N in AAA03208 (PubMed:7025207).Curated1
Sequence conflicti168D → G in AAA03208 (PubMed:7025207).Curated1
Sequence conflicti172Q → R in AAA03208 (PubMed:7025207).Curated1
Sequence conflicti175D → G in AAA03208 (PubMed:7025207).Curated1
Sequence conflicti180G → D in AAA03208 (PubMed:7025207).Curated1
Sequence conflicti584Q → H in AAA03208 (PubMed:7025207).Curated1
Sequence conflicti619Q → L in AAA03208 (PubMed:7025207).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75739.1.
AP009048 Genomic DNA. Translation: BAA16559.1.
J01581 Unassigned DNA. Translation: AAA03208.1.
L07596 Unassigned DNA. Translation: AAA71918.1. Sequence problems.
D44453 Genomic DNA. Translation: BAA21554.1.
Z28405 Genomic DNA. Translation: CAA82247.1.
PIRiE65049. SYECAT.
RefSeqiNP_417177.1. NC_000913.3.
WP_000047184.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75739; AAC75739; b2697.
BAA16559; BAA16559; BAA16559.
GeneIDi947175.
KEGGiecj:JW2667.
eco:b2697.
PATRICi32120790. VBIEscCol129921_2787.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75739.1.
AP009048 Genomic DNA. Translation: BAA16559.1.
J01581 Unassigned DNA. Translation: AAA03208.1.
L07596 Unassigned DNA. Translation: AAA71918.1. Sequence problems.
D44453 Genomic DNA. Translation: BAA21554.1.
Z28405 Genomic DNA. Translation: CAA82247.1.
PIRiE65049. SYECAT.
RefSeqiNP_417177.1. NC_000913.3.
WP_000047184.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3HXUX-ray2.10A2-442[»]
3HXVX-ray1.93A2-442[»]
3HXWX-ray1.93A2-442[»]
3HXXX-ray2.11A2-442[»]
3HXYX-ray2.27A2-442[»]
3HXZX-ray1.99A/B/C/D2-442[»]
3HY0X-ray1.90A/B2-442[»]
3HY1X-ray2.79A/B2-442[»]
ProteinModelPortaliP00957.
SMRiP00957.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi851507. 1 interactor.
DIPiDIP-9080N.
IntActiP00957. 19 interactors.
MINTiMINT-1266342.
STRINGi511145.b2697.

Protein family/group databases

MoonProtiP00957.

2D gel databases

SWISS-2DPAGEP00957.

Proteomic databases

EPDiP00957.
PaxDbiP00957.
PRIDEiP00957.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75739; AAC75739; b2697.
BAA16559; BAA16559; BAA16559.
GeneIDi947175.
KEGGiecj:JW2667.
eco:b2697.
PATRICi32120790. VBIEscCol129921_2787.

Organism-specific databases

EchoBASEiEB0033.
EcoGeneiEG10034. alaS.

Phylogenomic databases

eggNOGiENOG4105CIM. Bacteria.
COG0013. LUCA.
HOGENOMiHOG000156964.
InParanoidiP00957.
KOiK01872.
OMAiFDFNCPR.
PhylomeDBiP00957.

Enzyme and pathway databases

BioCyciEcoCyc:ALAS-MONOMER.
ECOL316407:JW2667-MONOMER.
MetaCyc:ALAS-MONOMER.
BRENDAi6.1.1.7. 2026.

Miscellaneous databases

EvolutionaryTraceiP00957.
PROiP00957.

Family and domain databases

HAMAPiMF_00036_B. Ala_tRNA_synth_B. 1 hit.
InterProiIPR002318. Ala-tRNA-lgiase_IIc.
IPR018162. Ala-tRNA-ligase_IIc_anticod-bd.
IPR018165. Ala-tRNA-synth_IIc_core.
IPR018164. Ala-tRNA-synth_IIc_N.
IPR023033. Ala_tRNA_ligase_euk/bac.
IPR003156. DHHA1_dom.
IPR018163. Thr/Ala-tRNA-synth_IIc_edit.
IPR009000. Transl_B-barrel.
IPR012947. tRNA_SAD.
[Graphical view]
PfamiPF02272. DHHA1. 1 hit.
PF01411. tRNA-synt_2c. 1 hit.
PF07973. tRNA_SAD. 1 hit.
[Graphical view]
PRINTSiPR00980. TRNASYNTHALA.
SMARTiSM00863. tRNA_SAD. 1 hit.
[Graphical view]
SUPFAMiSSF101353. SSF101353. 1 hit.
SSF50447. SSF50447. 1 hit.
SSF55186. SSF55186. 1 hit.
TIGRFAMsiTIGR00344. alaS. 1 hit.
PROSITEiPS50860. AA_TRNA_LIGASE_II_ALA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYA_ECOLI
AccessioniPrimary (citable) accession number: P00957
Secondary accession number(s): P78279
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 165 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.