ID   SYAP_ORYSJ              Reviewed;         996 AA.
AC   B9FSH5; Q654W2;
DT   30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT   22-JUL-2015, sequence version 2.
DT   03-AUG-2022, entry version 79.
DE   RecName: Full=Alanine--tRNA ligase, chloroplastic/mitochondrial {ECO:0000255|HAMAP-Rule:MF_03134};
DE            EC=6.1.1.7 {ECO:0000255|HAMAP-Rule:MF_03134};
DE   AltName: Full=Alanyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_03134};
DE            Short=AlaRS {ECO:0000255|HAMAP-Rule:MF_03134};
DE   Flags: Precursor;
GN   OrderedLocusNames=Os06g0245800, LOC_Os06g13660;
GN   ORFNames=OJ1136_C11.1, OsJ_20798;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
CC   -!- FUNCTION: Catalyzes the attachment of alanine to tRNA(Ala) in a two-
CC       step reaction: alanine is first activated by ATP to form Ala-AMP and
CC       then transferred to the acceptor end of tRNA(Ala). Also edits
CC       incorrectly charged tRNA(Ala) via its editing domain.
CC       {ECO:0000255|HAMAP-Rule:MF_03134}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-
CC         tRNA(Ala); Xref=Rhea:RHEA:12540, Rhea:RHEA-COMP:9657, Rhea:RHEA-
CC         COMP:9923, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57972,
CC         ChEBI:CHEBI:78442, ChEBI:CHEBI:78497, ChEBI:CHEBI:456215; EC=6.1.1.7;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03134};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03134};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_03134};
CC   -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_03134}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255|HAMAP-
CC       Rule:MF_03134}. Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03134}.
CC   -!- DOMAIN: Consists of three domains; the N-terminal catalytic domain, the
CC       editing domain and the C-terminal C-Ala domain. The editing domain
CC       removes incorrectly charged amino acids, while the C-Ala domain, along
CC       with tRNA(Ala), serves as a bridge to cooperatively bring together the
CC       editing and aminoacylation centers thus stimulating deacylation of
CC       misacylated tRNAs. {ECO:0000255|HAMAP-Rule:MF_03134}.
CC   -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC       {ECO:0000255|HAMAP-Rule:MF_03134}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAD45655.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAH93419.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=EEE65436.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AP004027; BAD45655.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008212; BAH93419.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014962; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000143; EEE65436.1; ALT_SEQ; Genomic_DNA.
DR   RefSeq; XP_015644249.1; XM_015788763.1.
DR   AlphaFoldDB; B9FSH5; -.
DR   SMR; B9FSH5; -.
DR   BioGRID; 1211216; 1.
DR   STRING; 4530.OS06T0245800-01; -.
DR   PaxDb; B9FSH5; -.
DR   PRIDE; B9FSH5; -.
DR   GeneID; 9266147; -.
DR   KEGG; osa:9266147; -.
DR   eggNOG; KOG0188; Eukaryota.
DR   InParanoid; B9FSH5; -.
DR   OrthoDB; 129373at2759; -.
DR   Proteomes; UP000000763; Chromosome 6.
DR   Proteomes; UP000007752; Chromosome 6.
DR   Proteomes; UP000059680; Chromosome 6.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0004813; F:alanine-tRNA ligase activity; IBA:GO_Central.
DR   GO; GO:0016597; F:amino acid binding; IBA:GO_Central.
DR   GO; GO:0002161; F:aminoacyl-tRNA editing activity; IBA:GO_Central.
DR   GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR   GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0006419; P:alanyl-tRNA aminoacylation; IBA:GO_Central.
DR   GO; GO:0006400; P:tRNA modification; IBA:GO_Central.
DR   Gene3D; 3.30.930.10; -; 1.
DR   HAMAP; MF_00036_B; Ala_tRNA_synth_B; 1.
DR   HAMAP; MF_03134; Ala_tRNA_synth_plantC; 1.
DR   InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR   InterPro; IPR002318; Ala-tRNA-lgiase_IIc.
DR   InterPro; IPR018162; Ala-tRNA-ligase_IIc_anticod-bd.
DR   InterPro; IPR018165; Ala-tRNA-synth_IIc_core.
DR   InterPro; IPR018164; Ala-tRNA-synth_IIc_N.
DR   InterPro; IPR023033; Ala_tRNA_ligase_euk/bac.
DR   InterPro; IPR027522; Ala_tRNA_synth_plant.
DR   InterPro; IPR003156; DHHA1_dom.
DR   InterPro; IPR018163; Thr/Ala-tRNA-synth_IIc_edit.
DR   InterPro; IPR009000; Transl_B-barrel_sf.
DR   InterPro; IPR012947; tRNA_SAD.
DR   Pfam; PF02272; DHHA1; 1.
DR   Pfam; PF01411; tRNA-synt_2c; 1.
DR   Pfam; PF07973; tRNA_SAD; 1.
DR   PRINTS; PR00980; TRNASYNTHALA.
DR   SMART; SM00863; tRNA_SAD; 1.
DR   SUPFAM; SSF101353; SSF101353; 1.
DR   SUPFAM; SSF50447; SSF50447; 1.
DR   SUPFAM; SSF55186; SSF55186; 1.
DR   SUPFAM; SSF55681; SSF55681; 1.
DR   TIGRFAMs; TIGR00344; alaS; 1.
DR   PROSITE; PS50860; AA_TRNA_LIGASE_II_ALA; 1.
PE   3: Inferred from homology;
KW   Aminoacyl-tRNA synthetase; ATP-binding; Chloroplast; Ligase; Metal-binding;
KW   Mitochondrion; Nucleotide-binding; Plastid; Protein biosynthesis;
KW   Reference proteome; RNA-binding; Transit peptide; tRNA-binding; Zinc.
FT   TRANSIT         1..?
FT                   /note="Chloroplast and mitochondrion"
FT   CHAIN           ?..996
FT                   /note="Alanine--tRNA ligase, chloroplastic/mitochondrial"
FT                   /id="PRO_0000402306"
FT   BINDING         677
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03134"
FT   BINDING         681
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03134"
FT   BINDING         779
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03134"
FT   BINDING         783
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03134"
SQ   SEQUENCE   996 AA;  108165 MW;  D191A91564D213A4 CRC64;
     MEAAALLSPT ATSRSPLPLL STAPAAHRLH VLLPLSGRRR RLCLRSSPRP RGSLGCAGDC
     VVRSMGSSRE RGVLVKTSSS SASVESATQE VGAASSGEWS GDAIRRRFLD FYAARGHKIL
     PSSSLVPDDP TVFLTIAGML QFKPIFLGKE PRRVPCATTS QKCIRTNDIE NVGRTSRHQT
     FFEMLGNFSF GDYFKKEAIT WAWELTTKEF GLPPERLWIS VFQDDDEAFS IWHNEVGVPK
     ERIKRLGEDD NFWTSGATGP CGPCSEIYYD FYPERGSSDA DLGDDSRFIE FYNLVFMQYN
     KKDDGSLEPL KQKNIDTGMG LERMARILQK VPNNYETDLI FPIIEKAASM ALVSYTTADD
     AMKTNLKIIG DHMRAVVYLI SDGVIPSNIG RGYVVRRLIR RVVRTGRLIG IRGDGHGNSE
     GAFLPSLAEV AISLSTEIDP DVESRRKSIL GELQREELRF VQTLERGEKL LDELLDEALS
     SAGNNGGKPC LSGKDVFLLY DTYGFPVEIT AEISGERGVI VDMKGFDMEM ENQRKQSQAA
     HNVVKLSVGN ETEIVKSIPD TEFLGYDSLS ATAVVKGLLV NGNSVNVVSE GSDVEIFLDR
     TPFYAESGGQ VGDNGFLYVY GEEDAKQKAV IEINDVQKSL GNIFVHKGTI KQGSVEVGKE
     IDAAVDAKLR QGAKAHHTAT HLLQSALKSI IGSETSQAGS LVAFDRLRFD FNFHRPLSEE
     ELMKIESLVN QWVSSATHLE TKVMDLQDAK NAGAIAMFGE KYGEQVRVVE VPGVSMELCG
     GTHVSNTAEI RGFKIISEQG IASGVRRIEA VAGDAFVEYV CARDNYMRCL CSSLKVKAED
     VNGRVETILE ELRTTRNEVS SLRSKIAVLK AASLANKATT IDNTRVVVEN MGDVDADGLK
     SAAEYLVDTL EDPAAVILGS SPGDGKVSLV AAFSPGVVKM GIQAGKFVGG IAKLCGGGGG
     GKPNFAQAGG RKPENLPGAL EKARDEIVAA ISSKSS