Alanyl-tRNA synthetase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P00957 (SYA_ECOLI)

Last modified February 9, 2010. Version 106. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Alanyl-tRNA synthetase
    EC=6.1.1.7
Alternative name(s):
    Alanine--tRNA ligase
      Short name=AlaRS

Gene names

Name:	alaS
Synonyms:	lovB
Ordered Locus Names:	b2697, JW2667

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	876 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Catalytic activity	ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala). HAMAP MF_00036
Cofactor	Binds 1 zinc ion per subunit. HAMAP MF_00036
Subunit structure	Homotetramer. Ref.6
Subcellular location	Cytoplasm HAMAP MF_00036.
Domain	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. Ref.13
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family.

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Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Domain	Zinc-finger
Ligand	ATP-binding Metal-binding Nucleotide-binding RNA-binding Zinc tRNA-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	alanyl-tRNA aminoacylation Ref.6 Inferred from direct assay. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from direct assay. Source: UniProtKB
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell membrane Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP alanine-tRNA ligase activity Ref.6 Inferred from direct assay. Source: UniProtKB specific transcriptional repressor activity Inferred from direct assay. Source: UniProtKB tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Ref.11 Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.6

Chain

2 – 876

875

Alanyl-tRNA synthetase HAMAP MF_00036

PRO_0000075113

Regions

Zinc finger

179 – 192

C2H2-type HAMAP MF_00036

Region

2 – 461

460

Catalytic HAMAP MF_00036

Region

699 – 808

110

Important for oligomerization HAMAP MF_00036

Amino acid modifications

Modified residue

N6-acetyllysine Ref.12

Experimental info

Mutagenesis

179

C → S: Inactivates the enzyme. Ref.11

Mutagenesis

182

C → S: No inactivation. Ref.11

Mutagenesis

184

E → Q: No inactivation. Ref.11

Mutagenesis

188

D → N: No inactivation. Ref.11

Mutagenesis

189

H → Q: Inactivates the enzyme. Ref.11

Mutagenesis

191

D → N: No inactivation. Ref.11

Mutagenesis

192

H → Q: Inactivates the enzyme. Ref.11

Sequence conflict

29 – 33

LVPHN → RYHIT Ref.4

Sequence conflict

29 – 33

LVPHN → RYHIT Ref.5

Sequence conflict

158

G → N Ref.4

Sequence conflict

158

G → N Ref.5

Sequence conflict

168

D → G in AAA03208. Ref.5

Sequence conflict

172

Q → R in AAA03208. Ref.5

Sequence conflict

175

D → G in AAA03208. Ref.5

Sequence conflict

180

G → D in AAA03208. Ref.5

Sequence conflict

584

Q → H in AAA03208. Ref.5

Sequence conflict

619

Q → L in AAA03208. Ref.5

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Sequences

Sequence

Length

Mass (Da)

Tools

P00957-1 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 73F69C69FCF8C08C
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FASTA

876

96,032

        10         20         30         40         50         60 
MSKSTAEIRQ AFLDFFHSKG HQVVASSSLV PHNDPTLLFT NAGMNQFKDV FLGLDKRNYS 

        70         80         90        100        110        120 
RATTSQRCVR AGGKHNDLEN VGYTARHHTF FEMLGNFSFG DYFKHDAIQF AWELLTSEKW 

       130        140        150        160        170        180 
FALPKERLWV TVYESDDEAY EIWEKEVGIP RERIIRIGDN KGAPYASDNF WQMGDTGPCG 

       190        200        210        220        230        240 
PCTEIFYDHG DHIWGGPPGS PEEDGDRYIE IWNIVFMQFN RQADGTMEPL PKPSVDTGMG 

       250        260        270        280        290        300 
LERIAAVLQH VNSNYDIDLF RTLIQAVAKV TGATDLSNKS LRVIADHIRS CAFLIADGVM 

       310        320        330        340        350        360 
PSNENRGYVL RRIIRRAVRH GNMLGAKETF FYKLVGPLID VMGSAGEDLK RQQAQVEQVL 

       370        380        390        400        410        420 
KTEEEQFART LERGLALLDE ELAKLSGDTL DGETAFRLYD TYGFPVDLTA DVCRERNIKV 

       430        440        450        460        470        480 
DEAGFEAAME EQRRRAREAS GFGADYNAMI RVDSASEFKG YDHLELNGKV TALFVDGKAV 

       490        500        510        520        530        540 
DAINAGQEAV VVLDQTPFYA ESGGQVGDKG ELKGANFSFA VEDTQKYGQA IGHIGKLAAG 

       550        560        570        580        590        600 
SLKVGDAVQA DVDEARRARI RLNHSATHLM HAALRQVLGT HVSQKGSLVN DKVLRFDFSH 

       610        620        630        640        650        660 
NEAMKPEEIR AVEDLVNTQI RRNLPIETNI MDLEAAKAKG AMALFGEKYD ERVRVLSMGD 

       670        680        690        700        710        720 
FSTELCGGTH ASRTGDIGLF RIISESGTAA GVRRIEAVTG EGAIATVHAD SDRLSEVAHL 

       730        740        750        760        770        780 
LKGDSNNLAD KVRSVLERTR QLEKELQQLK EQAAAQESAN LSSKAIDVNG VKLLVSELSG 

       790        800        810        820        830        840 
VEPKMLRTMV DDLKNQLGST IIVLATVVEG KVSLIAGVSK DVTDRVKAGE LIGMVAQQVG 

       850        860        870 
GKGGGRPDMA QAGGTDAAAL PAALASVKGW VSAKLQ

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Mass spectra of partial protein hydrolysates as a multiple phase check for long polypeptides deduced from DNA sequences: NH2-terminal segment of alanine tRNA synthetase." Herlihy W.C., Royal N.J., Biemann K., Putney S.D., Schimmel P.R. Proc. Natl. Acad. Sci. U.S.A. 77:6531-6535(1980) [PubMed: 7005898] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-166, PARTIAL PROTEIN SEQUENCE.
[5]	"Primary structure of a large aminoacyl-tRNA synthetase." Putney S.D., Royal N.J., de Vegvar H.N., Herlihy W.C., Biemann K., Schimmel P. Science 213:1497-1501(1981) [PubMed: 7025207] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 2-876.
[6]	"Purification and properties of alanine tRNA synthetase from Escherichia coli A tetramer of identical subunits." Putney S.D., Sauer R.T., Schimmel P.R. J. Biol. Chem. 256:198-204(1981) [PubMed: 7005211] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-12, SUBUNIT.
[7]	"Acceptor helix interactions in a class II tRNA synthetase: photoaffinity cross-linking of an RNA miniduplex substrate." Musier-Forsyth K., Schimmel P. Biochemistry 33:773-779(1994) [PubMed: 8292605] [Abstract] Cited for: PROTEIN SEQUENCE OF 163-173.
[8]	"Evidence for involvement of Escherichia coli genes pmbA, csrA and a previously unrecognized gene tldD, in the control of DNA gyrase by letD (ccdB) of sex factor F." Murayama N., Shimizu H., Takiguchi S., Baba Y., Amino H., Horiuchi T., Sekimizu K., Miki T. J. Mol. Biol. 256:483-502(1996) [PubMed: 8604133] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 799-876. Strain: KP4714.
[9]	"Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties." Romeo T., Gong M., Liu M.-Y., Brun-Zinkernagel A.-M. J. Bacteriol. 175:4744-4755(1993) [PubMed: 8393005] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 866-876. Strain: K12.
[10]	"Cloning, partial sequencing, and in vitro transcription of the gene for alanine tRNA synthetase." Putney S.D., Melendez D.L., Schimmel P.R. J. Biol. Chem. 256:205-211(1981) [PubMed: 6256345] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-13.
[11]	"Evidence for a 'cysteine-histidine box' metal-binding site in an Escherichia coli aminoacyl-tRNA synthetase." Miller W.T., Hill K.A.W., Schimmel P. Biochemistry 30:6970-6976(1991) [PubMed: 1712632] [Abstract] Cited for: ZINC-BINDING, MUTAGENESIS OF CYS-179; CYS-182; GLU-184; ASP-188; HIS-189; ASP-191 AND HIS-192.
[12]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-74, MASS SPECTROMETRY.
[13]	"The C-Ala domain brings together editing and aminoacylation functions on one tRNA." Guo M., Chong Y.E., Beebe K., Shapiro R., Yang X.-L., Schimmel P. Science 325:744-747(2009) [PubMed: 19661429] [Abstract] Cited for: FUNCTION IN TRNA-BINDING VIA C-ALA DOMAIN, DOMAIN EXCHANGE EXPERIMENTS.

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Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

SYECAT. E65049.

RefSeq

AP_003264.1.
NP_417177.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3HXU	X-ray	2.10	A	2-442	[»]
3HXV	X-ray	1.93	A	2-442	[»]
3HXW	X-ray	1.93	A	2-442	[»]
3HXX	X-ray	2.11	A	2-442	[»]
3HXY	X-ray	2.27	A	2-442	[»]
3HXZ	X-ray	1.99	A/B/C/D	2-442	[»]
3HY0	X-ray	1.90	A/B	2-442	[»]
3HY1	X-ray	2.79	A/B	2-442	[»]

SMR

P00957. Positions 2-464, 464-698.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9080N.

STRING

P00957.

2-D gel databases

SWISS-2DPAGE

P00957.

ECO2DBASE

F093.0. 6TH EDITION.

Proteomic databases

PRIDE

P00957.

Genome annotation databases

GeneID

947175.

GenomeReviews

Gene locus JW2667 in contig AP009048_GR.
Gene locus b2697 in contig U00096_GR.

KEGG

ecj:JW2667.
eco:b2697.

Organism-specific databases

EchoBASE

EB0033.

EcoGene

EG10034. alaS.

CMR

Search...

Phylogenomic databases

eggNOG

COG0013.

HOGENOM

HBG354397.

OMA

EIDIFRT.

Enzyme and pathway databases

BioCyc

EcoCyc:ALAS-MONOMER.
ECOL168927:B2697-MONOMER.
MetaCyc:ALAS-MONOMER.

Gene expression databases

Genevestigator

P00957.

Family and domain databases

HAMAP

MF_00036_B. Ala_tRNA_synth_B.
[Tree]

InterPro

IPR002318. Ala-tRNA-synth_IIc.
IPR018162. Ala-tRNA-synth_IIc_anticod-bd.
IPR018165. Ala-tRNA-synth_IIc_core.
IPR018164. Ala-tRNA-synth_IIc_N.
IPR003156. Pesterase_DHHA1.
IPR018163. Thr/Ala-tRNA-synth_IIc_edit.
IPR012947. tRNA_SAD.
[Graphical view]

Pfam

PF02272. DHHA1. 1 hit.
PF01411. tRNA-synt_2c. 1 hit.
PF07973. tRNA_SAD. 1 hit.
[Graphical view]

PRINTS

PR00980. TRNASYNTHALA.

SMART

SM00863. tRNA_SAD. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00344. alaS. 1 hit.

PROSITE

PS50860. AA_TRNA_LIGASE_II_ALA. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

SYA_ECOLI

Accession

Primary (citable) accession number: P00957
Secondary accession number(s): P78279

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	November 1, 1997
Last modified:	February 9, 2010
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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