SYA_AQUAE
ID SYA_AQUAE Reviewed; 867 AA.
AC O67323;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Alanine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00036};
DE EC=6.1.1.7 {ECO:0000255|HAMAP-Rule:MF_00036};
DE AltName: Full=Alanyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00036};
DE Short=AlaRS {ECO:0000255|HAMAP-Rule:MF_00036};
GN Name=alaS {ECO:0000255|HAMAP-Rule:MF_00036}; OrderedLocusNames=aq_1293;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF 1-454 WITH SUBSTRATES OR WITH
RP ATP.
RX PubMed=15657145; DOI=10.1073/pnas.0409024102;
RA Swairjo M.A., Schimmel P.R.;
RT "Breaking sieve for steric exclusion of a noncognate amino acid from active
RT site of a tRNA synthetase.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:988-993(2005).
RN [3]
RP DOMAIN EXCHANGE EXPERIMENTS, AND X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF
RP 758-867.
RX PubMed=19661429; DOI=10.1126/science.1174343;
RA Guo M., Chong Y.E., Beebe K., Shapiro R., Yang X.-L., Schimmel P.;
RT "The C-Ala domain brings together editing and aminoacylation functions on
RT one tRNA.";
RL Science 325:744-747(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 Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing
CC domain. {ECO:0000255|HAMAP-Rule:MF_00036}.
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_00036};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00036};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00036};
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
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. The Aquifex aeolicus domain can be used in vitro to
CC replace the corresponding domain in E.coli. {ECO:0000255|HAMAP-
CC Rule:MF_00036, ECO:0000269|PubMed:19661429}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000255|HAMAP-Rule:MF_00036}.
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DR EMBL; AE000657; AAC07289.1; -; Genomic_DNA.
DR PIR; H70411; H70411.
DR RefSeq; NP_213887.1; NC_000918.1.
DR RefSeq; WP_010880825.1; NC_000918.1.
DR PDB; 1RIQ; X-ray; 2.14 A; A=1-454.
DR PDB; 1YFR; X-ray; 2.15 A; A/B=1-454.
DR PDB; 1YFS; X-ray; 2.08 A; A/B=1-454.
DR PDB; 1YFT; X-ray; 2.23 A; A=1-454.
DR PDB; 1YGB; X-ray; 2.48 A; A=1-454.
DR PDB; 3G98; X-ray; 1.85 A; A/B=758-867.
DR PDB; 3HTZ; X-ray; 2.50 A; A=2-454.
DR PDBsum; 1RIQ; -.
DR PDBsum; 1YFR; -.
DR PDBsum; 1YFS; -.
DR PDBsum; 1YFT; -.
DR PDBsum; 1YGB; -.
DR PDBsum; 3G98; -.
DR PDBsum; 3HTZ; -.
DR AlphaFoldDB; O67323; -.
DR SMR; O67323; -.
DR STRING; 224324.aq_1293; -.
DR PRIDE; O67323; -.
DR EnsemblBacteria; AAC07289; AAC07289; aq_1293.
DR KEGG; aae:aq_1293; -.
DR PATRIC; fig|224324.8.peg.1011; -.
DR eggNOG; COG0013; Bacteria.
DR HOGENOM; CLU_004485_1_1_0; -.
DR InParanoid; O67323; -.
DR OMA; YHHTMFE; -.
DR OrthoDB; 91428at2; -.
DR BRENDA; 6.1.1.7; 396.
DR EvolutionaryTrace; O67323; -.
DR Proteomes; UP000000798; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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 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 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Metal-binding; Nucleotide-binding; Protein biosynthesis;
KW Reference proteome; RNA-binding; tRNA-binding; Zinc.
FT CHAIN 1..867
FT /note="Alanine--tRNA ligase"
FT /id="PRO_0000075047"
FT BINDING 559
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00036"
FT BINDING 563
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00036"
FT BINDING 661
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00036"
FT BINDING 665
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00036"
FT HELIX 5..17
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:1YFR"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:1RIQ"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 60..69
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 81..83
FT /evidence="ECO:0007829|PDB:3HTZ"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 89..101
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 104..117
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 126..131
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 135..142
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 143..145
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 149..151
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 152..155
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 161..179
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:1YGB"
FT HELIX 186..189
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 190..203
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:1YGB"
FT STRAND 209..222
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 223..230
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 236..238
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 240..242
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 243..253
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:1YFR"
FT HELIX 261..282
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 291..309
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 317..328
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 329..331
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 334..373
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:1YFR"
FT HELIX 381..389
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 395..403
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 404..406
FT /evidence="ECO:0007829|PDB:1YFS"
FT HELIX 411..423
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 424..426
FT /evidence="ECO:0007829|PDB:1YFS"
FT STRAND 443..445
FT /evidence="ECO:0007829|PDB:1YGB"
FT HELIX 446..449
FT /evidence="ECO:0007829|PDB:1YFS"
FT TURN 450..452
FT /evidence="ECO:0007829|PDB:1RIQ"
FT STRAND 758..762
FT /evidence="ECO:0007829|PDB:3G98"
FT STRAND 765..774
FT /evidence="ECO:0007829|PDB:3G98"
FT HELIX 777..787
FT /evidence="ECO:0007829|PDB:3G98"
FT STRAND 790..802
FT /evidence="ECO:0007829|PDB:3G98"
FT STRAND 805..812
FT /evidence="ECO:0007829|PDB:3G98"
FT HELIX 814..816
FT /evidence="ECO:0007829|PDB:3G98"
FT TURN 817..819
FT /evidence="ECO:0007829|PDB:3G98"
FT HELIX 822..832
FT /evidence="ECO:0007829|PDB:3G98"
FT STRAND 841..849
FT /evidence="ECO:0007829|PDB:3G98"
FT HELIX 851..853
FT /evidence="ECO:0007829|PDB:3G98"
FT HELIX 854..866
FT /evidence="ECO:0007829|PDB:3G98"
SQ SEQUENCE 867 AA; 98436 MW; E38C6D376643A149 CRC64;
MSLSAHEIRE LFLSFFEKKG HTRVKSAPLV PENDPTLLFV NAGMVPFKNV FLGLEKRPYK
RATSCQKCLR VSGKHNDLEQ VGYTSRHHTF FEMLGNFSFG DYFKKEAIEY AWEFVTEVLK
LPKEKLYVSV YKDDEEAYRI WNEHIGIPSE RIWRLGEEDN FWQMGDVGPC GPSSEIYVDR
GEEYEGDERY LEIWNLVFMQ YNRDENGVLT PLPHPNIDTG MGLERIASVL QGKNSNFEID
IIFPLIQFGE EVSGKKYGEK FETDVALRVI ADHLRAITFA ISDGVIPSNE GRGYVIRRIL
RRAMRFGYKL GIENPFLYKG VDLVVDIMKE PYPELELSRE FVKGIVKGEE KRFIKTLKAG
MEYIQEVIQK ALEEGRKTLS GKEVFTAYDT YGFPVDLIDE IAREKGLGID LEGFQCELEE
QRERARKHFK VEAKKVKPVY SHLKELGKTS AFVGYEHMEW ESQVVGLVKG EGLVSELKEG
EEGEVVLKET PFYPEGGGQI GDAGIIESDK ALFKVEDTQK PTEGIIVHIG KVLKGTLKVG
DTVHARVDKE RRWDIMRNHT ATHLLHAALR NVLGEHVRQA GSLVADKYLR FDFTHFSALT
EEELKRVEEL VNEKIRENLP VNVMEMAYDE ALKTGAIAIF EEKYGERVRV ISCGEFSKEL
CGGTHVSATG DIGYFKIISE SSVGAGVRRI VAQTGRWSVE TAFKEHQTLK KASSALGVGE
EEVIQKIEEL KEEIKDRERE IQRLKQELLK LQIREVVKEE NVGDFTLHYG VFEEVEPEEL
RNLADMLRQR TKKDVVFIAS RKGDKINFVI GVSKEISDKV NAKEVIREVG KVLKGGGGGR
ADLAQGGGKA PDKFPEAVKL LKEILSG
