SYA_YEAST
ID SYA_YEAST Reviewed; 983 AA.
AC P40825; D6W330;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2010, sequence version 3.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=Alanine--tRNA ligase, mitochondrial {ECO:0000255|HAMAP-Rule:MF_03133};
DE EC=6.1.1.7 {ECO:0000255|HAMAP-Rule:MF_03133};
DE AltName: Full=Alanyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_03133};
DE Short=AlaRS {ECO:0000255|HAMAP-Rule:MF_03133};
DE Flags: Precursor;
GN Name=ALA1 {ECO:0000255|HAMAP-Rule:MF_03133}; Synonyms=CDC64;
GN OrderedLocusNames=YOR335C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8896263;
RX DOI=10.1002/(sici)1097-0061(199609)12:10b<999::aid-yea976>3.0.co;2-e;
RA Parle-McDermott A.G., Hand N.J., Goulding S.E., Wolfe K.H.;
RT "Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces
RT cerevisiae chromosome XV: similarity to part of chromosome I.";
RL Yeast 12:999-1004(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 4-983, AND FUNCTION.
RX PubMed=7761427; DOI=10.1073/pnas.92.11.4932;
RA Ripmaster T.L., Shiba K., Schimmel P.;
RT "Wide cross-species aminoacyl-tRNA synthetase replacement in vivo: yeast
RT cytoplasmic alanine enzyme replaced by human polymyositis serum antigen.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:4932-4936(1995).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14576278; DOI=10.1073/pnas.2135385100;
RA Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E.,
RA Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P.,
RA Pfanner N., Meisinger C.;
RT "The proteome of Saccharomyces cerevisiae mitochondria.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003).
RN [8]
RP ALTERNATIVE INITIATION.
RX PubMed=15358761; DOI=10.1074/jbc.m408081200;
RA Tang H.L., Yeh L.S., Chen N.K., Ripmaster T., Schimmel P., Wang C.C.;
RT "Translation of a yeast mitochondrial tRNA synthetase initiated at
RT redundant non-AUG codons.";
RL J. Biol. Chem. 279:49656-49663(2004).
RN [9]
RP SUBCELLULAR LOCATION.
RX PubMed=16556230; DOI=10.1111/j.1365-2958.2006.05083.x;
RA Huang H.Y., Tang H.L., Chao H.Y., Yeh L.S., Wang C.C.;
RT "An unusual pattern of protein expression and localization of yeast alanyl-
RT tRNA synthetase isoforms.";
RL Mol. Microbiol. 60:189-198(2006).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-504, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-975, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
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_03133, ECO:0000269|PubMed:7761427}.
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_03133};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03133};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_03133};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_03133}.
CC -!- SUBCELLULAR LOCATION: [Isoform Cytoplasmic]: Cytoplasm.
CC -!- SUBCELLULAR LOCATION: [Isoform Mitochondrial]: Mitochondrion.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=Mitochondrial;
CC IsoId=P40825-1; Sequence=Displayed;
CC Name=Cytoplasmic;
CC IsoId=P40825-2; Sequence=VSP_040236;
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_03133}.
CC -!- MISCELLANEOUS: Present with 33800 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- MISCELLANEOUS: [Isoform Mitochondrial]: Produced by alternative
CC initiation at 2 upstream redundant non-AUG codons in-frame of the first
CC AUG used for isoform Cytoplasmic.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000255|HAMAP-Rule:MF_03133}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC49007.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA89980.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA99658.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=DAA11096.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; Z49821; CAA89980.1; ALT_INIT; Genomic_DNA.
DR EMBL; Z75243; CAA99658.1; ALT_INIT; Genomic_DNA.
DR EMBL; U18672; AAC49007.1; ALT_INIT; Genomic_DNA.
DR EMBL; BK006948; DAA11096.1; ALT_INIT; Genomic_DNA.
DR PIR; S62065; S62065.
DR RefSeq; NP_014980.3; NM_001183755.3. [P40825-2]
DR AlphaFoldDB; P40825; -.
DR SMR; P40825; -.
DR BioGRID; 34718; 351.
DR DIP; DIP-6286N; -.
DR IntAct; P40825; 10.
DR MINT; P40825; -.
DR STRING; 4932.YOR335C; -.
DR CarbonylDB; P40825; -.
DR iPTMnet; P40825; -.
DR MaxQB; P40825; -.
DR PaxDb; P40825; -.
DR PRIDE; P40825; -.
DR EnsemblFungi; YOR335C_mRNA; YOR335C; YOR335C. [P40825-2]
DR GeneID; 854513; -.
DR KEGG; sce:YOR335C; -.
DR SGD; S000005862; ALA1.
DR eggNOG; KOG0188; Eukaryota.
DR GeneTree; ENSGT00940000157335; -.
DR HOGENOM; CLU_004485_5_0_1; -.
DR InParanoid; P40825; -.
DR OMA; YHHTMFE; -.
DR BioCyc; YEAST:G3O-33810-MON; -.
DR BRENDA; 6.1.1.7; 984.
DR PRO; PR:P40825; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; P40825; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0004813; F:alanine-tRNA ligase activity; IMP:SGD.
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; IMP:SGD.
DR GO; GO:0070143; P:mitochondrial alanyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
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 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; 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 1: Evidence at protein level;
KW Alternative initiation; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm;
KW Ligase; Metal-binding; Mitochondrion; Nucleotide-binding; Phosphoprotein;
KW Protein biosynthesis; Reference proteome; RNA-binding; Transit peptide;
KW tRNA-binding; Zinc.
FT TRANSIT 1..24
FT /note="Mitochondrion"
FT CHAIN 25..983
FT /note="Alanine--tRNA ligase, mitochondrial"
FT /id="PRO_0000075287"
FT BINDING 625
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03133"
FT BINDING 629
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03133"
FT BINDING 744
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03133"
FT BINDING 748
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03133"
FT MOD_RES 504
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 975
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT VAR_SEQ 1..25
FT /note="Missing (in isoform Cytoplasmic)"
FT /evidence="ECO:0000305"
FT /id="VSP_040236"
FT CONFLICT 4..7
FT /note="TTGL -> NYRI (in Ref. 4; AAC49007)"
FT /evidence="ECO:0000305"
FT CONFLICT 16
FT /note="Missing (in Ref. 4; AAC49007)"
FT /evidence="ECO:0000305"
FT CONFLICT 161
FT /note="R -> S (in Ref. 4; AAC49007)"
FT /evidence="ECO:0000305"
FT CONFLICT 490..492
FT /note="KDQ -> RTK (in Ref. 4; AAC49007)"
FT /evidence="ECO:0000305"
FT CONFLICT 865..866
FT /note="FE -> LQ (in Ref. 4; AAC49007)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 983 AA; 110059 MW; DC0F50DB6409F11F CRC64;
MTSTTGLRNL TLSFKKQLTT STRTIMTIGD KQKWTATNVR NTFLDYFKSK EHKFVKSSPV
VPFDDPTLLF ANAGMNQYKP IFLGTVDPAS DFYTLKRAYN SQKCIRAGGK HNDLEDVGKD
SYHHTFFEML GNWSFGDYFK KEAITYSWTL LTEVYGIPKD RLYVTYFEGD EKLGLEPDTE
ARELWKNVGV PDDHILPGNA KDNFWEMGDQ GPCGPCSEIH YDRIGGRNAA SLVNMDDPDV
LEVWNLVFIQ FNREQDGSLK PLPAKHIDTG MGFERLVSVL QDVRSNYDTD VFTPLFERIQ
EITSVRPYSG NFGENDKDGI DTAYRVLADH VRTLTFALAD GGVPNNEGRG YVLRRILRRG
ARYARKYMNY PIGNFFSTLA PTLISQVQDI FPELAKDPAF LFEILDEEEA SFAKTLDRGE
RLFEKYASAA SKTESKTLDG KQVWRLYDTY GFPVDLTELM AEEQGLKIDG PGFEKAKQES
YEASKRGGKK DQSDLIKLNV HELSELNDAK VPKTNDEFKY GSANVEGTIL KLHDGTNFVD
EITEPGKKYG IILDKTCFYA EQGGQEYDTG KIVIDDAAEF NVENVQLYNG FVFHTGSLEE
GKLSVGDKII ASFDELRRFP IKNNHTGTHI LNFALKETLG NDVDQKGSLV APEKLRFDFS
HKKAVSNEEL KKVEDICNEQ IKENLQVFYK EIPLDLAKSI DGVRAVFGET YPDPVRVVSV
GKPIEELLAN PANEEWTKYS IEFCGGTHVN KTGDIKYFVI LEESGIAKGI RRIVAVTGTE
AFEAQRLAEQ FAADLDAADK LPFSPIKEKK LKELGVKLGQ LSISVITKNE LKQKFNKIEK
AVKDEVKSRA KKENKQTLDE VKTFFETNEN APYLVKFIDI SPNAKAITEA INYMKSNDSV
KDKSIYLLAG NDPEGRVAHG CYISNAALAK GIDGSALAKK VSSIIGGKAG GKGNVFQGMG
DKPAAIKDAV DDLESLFKEK LSI
