P40825 (SYA_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Alanine--tRNA ligase, mitochondrial
EC=6.1.1.7

Alternative name(s):
Alanyl-tRNA synthetase
Short name=AlaRS

Gene names

Name:	ALA1
Synonyms:	CDC64
Ordered Locus Names:	YOR335C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	983 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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). Also edits incorrectly charged tRNA(Ala) via its editing domain By similarity. Ref.4
Catalytic activity	ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala). HAMAP-Rule MF_03133
Cofactor	Binds 1 zinc ion per subunit Potential.
Subunit structure	Monomer By similarity.
Subcellular location	Isoform Cytoplasmic: Cytoplasm Ref.5 Ref.7 Ref.9. Isoform Mitochondrial: Mitochondrion Ref.5 Ref.7 Ref.9.
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-Rule MF_03133
Miscellaneous	Present with 33800 molecules/cell in log phase SD medium. HAMAP-Rule MF_03133
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family.
Sequence caution	The sequence AAC49007.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence CAA89980.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence CAA99658.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended. The sequence DAA11096.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm Mitochondrion
Coding sequence diversity	Alternative initiation
Domain	Transit peptide
Ligand	ATP-binding Metal-binding Nucleotide-binding RNA-binding Zinc tRNA-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mitochondrial alanyl-tRNA aminoacylation Inferred by curator Ref.9. Source: SGD
Cellular_component	mitochondrion Inferred from direct assay Ref.7Ref.9PubMed 16823961. Source: SGD
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW alanine-tRNA ligase activity Inferred from genetic interaction Ref.4. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]

Isoform Mitochondrial (identifier: P40825-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Produced by alternative initiation at 2 upstream redundant non-AUG codons in-frame of the first AUG used for isoform Cytoplasmic.

Isoform Cytoplasmic (identifier: P40825-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-25: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 24	24	Mitochondrion HAMAP-Rule MF_03133
	Chain	25 – 983	959	Alanine--tRNA ligase, mitochondrial HAMAP-Rule MF_03133		PRO_0000075287
Sites
	Metal binding	625	1	Zinc Potential
	Metal binding	629	1	Zinc Potential
	Metal binding	744	1	Zinc Potential
	Metal binding	748	1	Zinc Potential
Amino acid modifications
	Modified residue	504	1	Phosphoserine Ref.11
	Modified residue	975	1	Phosphoserine Ref.10 Ref.11
Natural variations
	Alternative sequence	1 – 25	25	Missing in isoform Cytoplasmic.		VSP_040236
Experimental info
	Sequence conflict	4 – 7	4	TTGL → NYRI in AAC49007. Ref.4
	Sequence conflict	16	1	Missing in AAC49007. Ref.4
	Sequence conflict	161	1	R → S in AAC49007. Ref.4
	Sequence conflict	490 – 492	3	KDQ → RTK in AAC49007. Ref.4
	Sequence conflict	865 – 866	2	FE → LQ in AAC49007. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Isoform Mitochondrial [UniParc]. Last modified November 30, 2010. Version 3. Checksum: DC0F50DB6409F11F	FASTA	983	110,059
	10 20 30 40 50 60 MTSTTGLRNL TLSFKKQLTT STRTIMTIGD KQKWTATNVR NTFLDYFKSK EHKFVKSSPV 70 80 90 100 110 120 VPFDDPTLLF ANAGMNQYKP IFLGTVDPAS DFYTLKRAYN SQKCIRAGGK HNDLEDVGKD 130 140 150 160 170 180 SYHHTFFEML GNWSFGDYFK KEAITYSWTL LTEVYGIPKD RLYVTYFEGD EKLGLEPDTE 190 200 210 220 230 240 ARELWKNVGV PDDHILPGNA KDNFWEMGDQ GPCGPCSEIH YDRIGGRNAA SLVNMDDPDV 250 260 270 280 290 300 LEVWNLVFIQ FNREQDGSLK PLPAKHIDTG MGFERLVSVL QDVRSNYDTD VFTPLFERIQ 310 320 330 340 350 360 EITSVRPYSG NFGENDKDGI DTAYRVLADH VRTLTFALAD GGVPNNEGRG YVLRRILRRG 370 380 390 400 410 420 ARYARKYMNY PIGNFFSTLA PTLISQVQDI FPELAKDPAF LFEILDEEEA SFAKTLDRGE 430 440 450 460 470 480 RLFEKYASAA SKTESKTLDG KQVWRLYDTY GFPVDLTELM AEEQGLKIDG PGFEKAKQES 490 500 510 520 530 540 YEASKRGGKK DQSDLIKLNV HELSELNDAK VPKTNDEFKY GSANVEGTIL KLHDGTNFVD 550 560 570 580 590 600 EITEPGKKYG IILDKTCFYA EQGGQEYDTG KIVIDDAAEF NVENVQLYNG FVFHTGSLEE 610 620 630 640 650 660 GKLSVGDKII ASFDELRRFP IKNNHTGTHI LNFALKETLG NDVDQKGSLV APEKLRFDFS 670 680 690 700 710 720 HKKAVSNEEL KKVEDICNEQ IKENLQVFYK EIPLDLAKSI DGVRAVFGET YPDPVRVVSV 730 740 750 760 770 780 GKPIEELLAN PANEEWTKYS IEFCGGTHVN KTGDIKYFVI LEESGIAKGI RRIVAVTGTE 790 800 810 820 830 840 AFEAQRLAEQ FAADLDAADK LPFSPIKEKK LKELGVKLGQ LSISVITKNE LKQKFNKIEK 850 860 870 880 890 900 AVKDEVKSRA KKENKQTLDE VKTFFETNEN APYLVKFIDI SPNAKAITEA INYMKSNDSV 910 920 930 940 950 960 KDKSIYLLAG NDPEGRVAHG CYISNAALAK GIDGSALAKK VSSIIGGKAG GKGNVFQGMG 970 980 DKPAAIKDAV DDLESLFKEK LSI
	Isoform Cytoplasmic [UniParc]. Checksum: 50FD31C2E2D40F32	FASTA	958	107,277
	10 20 30 40 50 60 MTIGDKQKWT ATNVRNTFLD YFKSKEHKFV KSSPVVPFDD PTLLFANAGM NQYKPIFLGT 70 80 90 100 110 120 VDPASDFYTL KRAYNSQKCI RAGGKHNDLE DVGKDSYHHT FFEMLGNWSF GDYFKKEAIT 130 140 150 160 170 180 YSWTLLTEVY GIPKDRLYVT YFEGDEKLGL EPDTEARELW KNVGVPDDHI LPGNAKDNFW 190 200 210 220 230 240 EMGDQGPCGP CSEIHYDRIG GRNAASLVNM DDPDVLEVWN LVFIQFNREQ DGSLKPLPAK 250 260 270 280 290 300 HIDTGMGFER LVSVLQDVRS NYDTDVFTPL FERIQEITSV RPYSGNFGEN DKDGIDTAYR 310 320 330 340 350 360 VLADHVRTLT FALADGGVPN NEGRGYVLRR ILRRGARYAR KYMNYPIGNF FSTLAPTLIS 370 380 390 400 410 420 QVQDIFPELA KDPAFLFEIL DEEEASFAKT LDRGERLFEK YASAASKTES KTLDGKQVWR 430 440 450 460 470 480 LYDTYGFPVD LTELMAEEQG LKIDGPGFEK AKQESYEASK RGGKKDQSDL IKLNVHELSE 490 500 510 520 530 540 LNDAKVPKTN DEFKYGSANV EGTILKLHDG TNFVDEITEP GKKYGIILDK TCFYAEQGGQ 550 560 570 580 590 600 EYDTGKIVID DAAEFNVENV QLYNGFVFHT GSLEEGKLSV GDKIIASFDE LRRFPIKNNH 610 620 630 640 650 660 TGTHILNFAL KETLGNDVDQ KGSLVAPEKL RFDFSHKKAV SNEELKKVED ICNEQIKENL 670 680 690 700 710 720 QVFYKEIPLD LAKSIDGVRA VFGETYPDPV RVVSVGKPIE ELLANPANEE WTKYSIEFCG 730 740 750 760 770 780 GTHVNKTGDI KYFVILEESG IAKGIRRIVA VTGTEAFEAQ RLAEQFAADL DAADKLPFSP 790 800 810 820 830 840 IKEKKLKELG VKLGQLSISV ITKNELKQKF NKIEKAVKDE VKSRAKKENK QTLDEVKTFF 850 860 870 880 890 900 ETNENAPYLV KFIDISPNAK AITEAINYMK SNDSVKDKSI YLLAGNDPEG RVAHGCYISN 910 920 930 940 950 AALAKGIDGS ALAKKVSSII GGKAGGKGNV FQGMGDKPAA IKDAVDDLES LFKEKLSI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I." Parle-McDermott A.G., Hand N.J., Goulding S.E., Wolfe K.H. Yeast 12:999-1004(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Wide cross-species aminoacyl-tRNA synthetase replacement in vivo: yeast cytoplasmic alanine enzyme replaced by human polymyositis serum antigen." Ripmaster T.L., Shiba K., Schimmel P. Proc. Natl. Acad. Sci. U.S.A. 92:4932-4936(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 4-983, FUNCTION.
[5]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[6]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"The proteome of Saccharomyces cerevisiae mitochondria." Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E., Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P., Pfanner N., Meisinger C. Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[8]	"Translation of a yeast mitochondrial tRNA synthetase initiated at redundant non-AUG codons." Tang H.L., Yeh L.S., Chen N.K., Ripmaster T., Schimmel P., Wang C.C. J. Biol. Chem. 279:49656-49663(2004) [PubMed] [Europe PMC] [Abstract] Cited for: ALTERNATIVE INITIATION.
[9]	"An unusual pattern of protein expression and localization of yeast alanyl-tRNA synthetase isoforms." Huang H.Y., Tang H.L., Chao H.Y., Yeh L.S., Wang C.C. Mol. Microbiol. 60:189-198(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[10]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-975, MASS SPECTROMETRY.
[11]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-504 AND SER-975, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z49821 Genomic DNA. Translation: CAA89980.1. Different initiation. Z75243 Genomic DNA. Translation: CAA99658.1. Different initiation. U18672 Genomic DNA. Translation: AAC49007.1. Different initiation. BK006948 Genomic DNA. Translation: DAA11096.1. Different initiation.
PIR	S62065.
RefSeq	NP_014980.3. NM_001183755.3.
3D structure databases
ProteinModelPortal	P40825.
SMR	P40825. Positions 29-778.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6286N.
IntAct	P40825. 10 interactions.
MINT	MINT-688621.
STRING	4932.YOR335C.
Proteomic databases
PaxDb	P40825.
PeptideAtlas	P40825.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	854513.
KEGG	sce:YOR335C. sce:YOR337W.
Organism-specific databases
CYGD	YOR335c.
SGD	S000005862. ALA1.
Phylogenomic databases
eggNOG	COG0013.
KO	K01872.
OMA	EWFDFPK.
OrthoDB	EOG44BF9B.
Gene expression databases
Genevestigator	P40825.
GermOnline	YOR335C. Saccharomyces cerevisiae.
Family and domain databases
HAMAP	MF_00036_B. Ala_tRNA_synth_B.
InterPro	IPR002318. 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. Pesterase_DHHA1. IPR018163. Thr/Ala-tRNA-synth_IIc_edit. IPR012947. tRNA_SAD. [Graphical view]
PANTHER	PTHR11777:SF6. PTHR11777:SF6. 1 hit.
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]
SUPFAM	SSF101353. Ala-tRNA-synth_IIc_anticod-bd. 1 hit. SSF55186. Thr/Ala-tRNA-synth_IIc_edit. 1 hit.
TIGRFAMs	TIGR00344. alaS. 1 hit.
PROSITE	PS50860. AA_TRNA_LIGASE_II_ALA. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	976870.

Entry information

Entry name

SYA_YEAST

Accession

Primary (citable) accession number: P40825
Secondary accession number(s): D6W330

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	November 30, 2010
Last modified:	May 1, 2013
This is version 116 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program