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O58035 (SYA_PYRHO) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 80. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Alanine--tRNA ligase
EC=6.1.1.7
Alternative name(s):
Alanyl-tRNA synthetase
Short name=AlaRS
Gene names
Name:alaS
Ordered Locus Names:PH0297
OrganismPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]
Taxonomic identifier70601 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length915 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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). Edits incorrectly charged Ser-tRNA(Ala). Incorrectly charged amino acids occur because the of inherent physicochemical limitations on discrimination between closely related amino acids (Gly and Ser) in the charging step. Ref.2

Catalytic activity

ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala). HAMAP MF_00036_A

Cofactor

Binds 1 zinc ion per subunit. Ref.3

Subunit structure

Homodimer Probable.

Subcellular location

Cytoplasm HAMAP MF_00036_A.

Domain

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 By similarity. HAMAP MF_00036_A

Sequence similarities

Belongs to the class-II aminoacyl-tRNA synthetase family.

Caution

Unlike the case in Archaeoglobus fulgidus and some of the free-standing tRNA(Ala) AlaX editing proteins, His-721 does not bind zinc but forms a hydrogen bond with Cys-717 instead.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 915915Alanine--tRNA ligase HAMAP MF_00036_A
PRO_0000075274

Sites

Metal binding6131Zinc
Metal binding6171Zinc
Metal binding7171Zinc

Experimental info

Mutagenesis6331Q → M: Significant deacylation of correctly charged L-alanyl-tRNA(Ala) occurs. Ref.2

Secondary structure

1 .................................................................................................... 915
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O58035 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: AFD4C26939928D33

FASTA915105,011
        10         20         30         40         50         60 
MEFIMKTRMF EEEGWIRKKC KVCGKPFWTL DPDRETCGDP PCDEYQFIGK PGIPRKYTLD 

        70         80         90        100        110        120 
EMREKFLRFF EKHEIYPHGR VKRYPVLPRW RDDVLLVGAS IMDFQPWVIS GEADPPANPL 

       130        140        150        160        170        180 
VISQPSIRFT DIDNVGITGR HFTIFEMMAH HAFNYPGKPI YWMDETVELA FEFFTKELKM 

       190        200        210        220        230        240 
KPEDITFKEN PWAGGGNAGP AFEVLYRGLE VATLVFMQYK KAPENAPQDQ VVVIKGEKYI 

       250        260        270        280        290        300 
PMETKVVDTG YGLERLVWMS QGTPTAYDAV LGYVVEPLKK MAGIEKIDEK ILMENSRLAG 

       310        320        330        340        350        360 
MFDIEDLGDL RYLREQVAKR VGITVEELEK AIRPYELIYA IADHTKALTF MLADGVVPSN 

       370        380        390        400        410        420 
VKAGYLARLL IRKSIRHLRE LGLEVPLSEI VALHIKELHK TFPEFKEMED IILEMIELEE 

       430        440        450        460        470        480 
KKYAETLRRG SDLVRREIAK LKKKGIKEIP VEKLVTFYES HGLTPEIVKE IAEKEGVKVN 

       490        500        510        520        530        540 
IPDNFYSMVA KEAERTKEEK GEELVDFELL KDLPDTRRLY YEDPFMKEFD AKVLRVIKDW 

       550        560        570        580        590        600 
VILDATAFYP EGGGQPYDTG VLIVNGREVK VTNVQKVGKV IIHKVEDPGA FKEGMIVHGK 

       610        620        630        640        650        660 
IDWKRRIQHM RHHTGTHVLM GALVRVLGRH VWQAGSQLTT DWARLDISHY KRISEEELKE 

       670        680        690        700        710        720 
IEMLANRIVM EDRKVTWEWL PRTTAEQKYG FRLYQGGVVP GREIRVVKIE DWDVQACGGT 

       730        740        750        760        770        780 
HLPSTGLVGP IKILRTERIQ DGVERIIFAC GEAAIREWQK ERDLLKKASN VLRVPPEKLP 

       790        800        810        820        830        840 
ETAERFFNEW KEARKEVDKL KKELARLLVY ELESKMQKIG SIEFIGEVVE GSMEDLRELV 

       850        860        870        880        890        900 
EKLKKPKRVV VLISRDGYFA VSVGSEVGVE ANELAKKITL IAGGGGGGRR DIAQGKVKDI 

       910 
SKAKDVIESI KSMFS

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3."
Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. expand/collapse author list , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.
DNA Res. 5:55-76(1998) [PubMed: 9679194] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
[2]"Molecular basis of alanine discrimination in editing site."
Sokabe M., Okada A., Yao M., Nakashima T., Tanaka I.
Proc. Natl. Acad. Sci. U.S.A. 102:11669-11674(2005) [PubMed: 16087889] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF GLN-633.
[3]"The structure of alanyl-tRNA synthetase with editing domain."
Sokabe M., Ose T., Nakamura A., Tokunaga K., Nureki O., Yao M., Tanaka I.
Proc. Natl. Acad. Sci. U.S.A. 106:11028-11033(2009) [PubMed: 19549823] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS) OF 1-752 IN THE PRESENCE AND ABSENCE OF AN ALANYL-ADENYLATE ANALOG, ZINC-BINDING, COFACTOR.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		BA000001 Genomic DNA. Translation: BAA29370.1.
PIRC71455.
RefSeqNP_142285.1. NC_000961.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2ZZEX-ray2.16A/B1-752[»]
2ZZFX-ray2.70A1-752[»]
2ZZGX-ray3.10A/B1-752[»]
ProteinModelPortalO58035.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaEBPYRT00000001158; EBPYRP00000001158; EBPYRG00000001158.
GeneID1444180.
GenomeReviewsGene locus PH0297 in contig BA000001_GR.
KEGGpho:PH0297.
NMPDRfig|70601.1.peg.280.

Organism-specific databases

CMRSearch...

Phylogenomic databases

GeneTreeEBGT00050000022658.
HOGENOMHBG392147.
OMAMFTNSGM.
PhylomeDBO58035.
ProtClustDBPRK13902.

Enzyme and pathway databases

BioCycPHOR70601:PH0297-MONOMER.

Family and domain databases

HAMAPMF_00036_A. Ala_tRNA_synth_A.
[Tree]
InterProIPR002318. Ala-tRNA-synth_IIc.
IPR018162. Ala-tRNA-synth_IIc_anticod-bd.
IPR018165. Ala-tRNA-synth_IIc_core.
IPR018164. Ala-tRNA-synth_IIc_N.
IPR022429. Ala-tRNA_synth_arc.
IPR003156. Pesterase_DHHA1.
IPR018163. Thr/Ala-tRNA-synth_IIc_edit.
IPR012947. tRNA_SAD.
[Graphical view]
KOK01872.
PANTHERPTHR11777:SF6. PTHR11777:SF6. 1 hit.
PfamPF02272. DHHA1. 1 hit.
PF01411. tRNA-synt_2c. 1 hit.
PF07973. tRNA_SAD. 1 hit.
[Graphical view]
PRINTSPR00980. TRNASYNTHALA.
SMARTSM00863. tRNA_SAD. 1 hit.
[Graphical view]
SUPFAMSSF101353. Ala-tRNA-synth_IIc_anticod-bd. 1 hit.
SSF55186. Thr/Ala-tRNA-synth_IIc_edit. 1 hit.
TIGRFAMsTIGR03683. A-tRNA_syn_arch. 1 hit.
TIGR00344. AlaS. 1 hit.
PROSITEPS50860. AA_TRNA_LIGASE_II_ALA. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameSYA_PYRHO
AccessionPrimary (citable) accession number: O58035
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: January 25, 2012
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents