SYA_PYRHO
ID SYA_PYRHO Reviewed; 915 AA.
AC O58035;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Alanine--tRNA ligase;
DE EC=6.1.1.7;
DE AltName: Full=Alanyl-tRNA synthetase;
DE Short=AlaRS;
GN Name=alaS; OrderedLocusNames=PH0297;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP FUNCTION, AND MUTAGENESIS OF GLN-633.
RX PubMed=16087889; DOI=10.1073/pnas.0502119102;
RA Sokabe M., Okada A., Yao M., Nakashima T., Tanaka I.;
RT "Molecular basis of alanine discrimination in editing site.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:11669-11674(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS) OF 1-752 IN THE PRESENCE AND ABSENCE
RP OF AN ALANYL-ADENYLATE ANALOG, ZINC-BINDING, AND COFACTOR.
RX PubMed=19549823; DOI=10.1073/pnas.0904645106;
RA Sokabe M., Ose T., Nakamura A., Tokunaga K., Nureki O., Yao M., Tanaka I.;
RT "The structure of alanyl-tRNA synthetase with editing domain.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:11028-11033(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). Edits incorrectly
CC charged Ser-tRNA(Ala). Incorrectly charged amino acids occur because
CC the of inherent physicochemical limitations on discrimination between
CC closely related amino acids (Gly and Ser) in the charging step.
CC {ECO:0000269|PubMed:16087889}.
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 -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:19549823};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:19549823};
CC -!- SUBUNIT: Homodimer. {ECO:0000305}.
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 (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
CC -!- CAUTION: Unlike the case in Archaeoglobus fulgidus and some of the
CC free-standing tRNA(Ala) AlaX editing proteins, His-721 does not bind
CC zinc but forms a hydrogen bond with Cys-717 instead. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000001; BAA29370.1; -; Genomic_DNA.
DR PIR; C71455; C71455.
DR RefSeq; WP_010884393.1; NC_000961.1.
DR PDB; 2ZZE; X-ray; 2.16 A; A/B=1-752.
DR PDB; 2ZZF; X-ray; 2.70 A; A=1-752.
DR PDB; 2ZZG; X-ray; 3.10 A; A/B=1-752.
DR PDBsum; 2ZZE; -.
DR PDBsum; 2ZZF; -.
DR PDBsum; 2ZZG; -.
DR AlphaFoldDB; O58035; -.
DR SMR; O58035; -.
DR STRING; 70601.3256687; -.
DR PRIDE; O58035; -.
DR EnsemblBacteria; BAA29370; BAA29370; BAA29370.
DR GeneID; 1444180; -.
DR KEGG; pho:PH0297; -.
DR eggNOG; arCOG01255; Archaea.
DR OMA; YHHTMFE; -.
DR OrthoDB; 7896at2157; -.
DR BRENDA; 6.1.1.7; 5244.
DR EvolutionaryTrace; O58035; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004813; F:alanine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0002161; F:aminoacyl-tRNA editing activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
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; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.930.10; -; 1.
DR HAMAP; MF_00036_A; Ala_tRNA_synth_A; 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; IPR022429; Ala-tRNA_lgiase_arc.
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; TIGR03683; A-tRNA_syn_arch; 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; RNA-binding;
KW tRNA-binding; Zinc.
FT CHAIN 1..915
FT /note="Alanine--tRNA ligase"
FT /id="PRO_0000075274"
FT BINDING 613
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 617
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT BINDING 717
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT MUTAGEN 633
FT /note="Q->M: Significant deacylation of correctly charged
FT L-alanyl-tRNA(Ala) occurs."
FT /evidence="ECO:0000269|PubMed:16087889"
FT HELIX 8..12
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 21..23
FT /evidence="ECO:0007829|PDB:2ZZF"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 40..42
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 48..50
FT /evidence="ECO:0007829|PDB:2ZZG"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 67..71
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:2ZZF"
FT HELIX 100..104
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 105..111
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 116..127
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 135..137
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 143..155
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 163..176
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 182..184
FT /evidence="ECO:0007829|PDB:2ZZF"
FT STRAND 185..189
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 201..206
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 209..216
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 234..236
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 237..241
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 245..252
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 253..261
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 272..278
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 289..300
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 304..308
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 310..321
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 325..353
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 359..361
FT /evidence="ECO:0007829|PDB:2ZZF"
FT HELIX 364..380
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 387..395
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 399..401
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 403..405
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 409..421
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 424..444
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 451..461
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 465..472
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 474..476
FT /evidence="ECO:0007829|PDB:2ZZG"
FT HELIX 485..490
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 491..494
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 507..513
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 519..522
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 529..531
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 533..537
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 540..546
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 560..564
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 567..569
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 571..575
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 582..585
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 588..590
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 597..601
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 606..627
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 632..638
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 643..648
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 655..658
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 661..671
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 675..681
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 682..687
FT /evidence="ECO:0007829|PDB:2ZZE"
FT HELIX 691..693
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 695..697
FT /evidence="ECO:0007829|PDB:2ZZG"
FT STRAND 701..709
FT /evidence="ECO:0007829|PDB:2ZZE"
FT TURN 710..712
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 713..716
FT /evidence="ECO:0007829|PDB:2ZZF"
FT HELIX 725..728
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 731..740
FT /evidence="ECO:0007829|PDB:2ZZE"
FT STRAND 743..750
FT /evidence="ECO:0007829|PDB:2ZZE"
SQ SEQUENCE 915 AA; 105011 MW; AFD4C26939928D33 CRC64;
MEFIMKTRMF EEEGWIRKKC KVCGKPFWTL DPDRETCGDP PCDEYQFIGK PGIPRKYTLD
EMREKFLRFF EKHEIYPHGR VKRYPVLPRW RDDVLLVGAS IMDFQPWVIS GEADPPANPL
VISQPSIRFT DIDNVGITGR HFTIFEMMAH HAFNYPGKPI YWMDETVELA FEFFTKELKM
KPEDITFKEN PWAGGGNAGP AFEVLYRGLE VATLVFMQYK KAPENAPQDQ VVVIKGEKYI
PMETKVVDTG YGLERLVWMS QGTPTAYDAV LGYVVEPLKK MAGIEKIDEK ILMENSRLAG
MFDIEDLGDL RYLREQVAKR VGITVEELEK AIRPYELIYA IADHTKALTF MLADGVVPSN
VKAGYLARLL IRKSIRHLRE LGLEVPLSEI VALHIKELHK TFPEFKEMED IILEMIELEE
KKYAETLRRG SDLVRREIAK LKKKGIKEIP VEKLVTFYES HGLTPEIVKE IAEKEGVKVN
IPDNFYSMVA KEAERTKEEK GEELVDFELL KDLPDTRRLY YEDPFMKEFD AKVLRVIKDW
VILDATAFYP EGGGQPYDTG VLIVNGREVK VTNVQKVGKV IIHKVEDPGA FKEGMIVHGK
IDWKRRIQHM RHHTGTHVLM GALVRVLGRH VWQAGSQLTT DWARLDISHY KRISEEELKE
IEMLANRIVM EDRKVTWEWL PRTTAEQKYG FRLYQGGVVP GREIRVVKIE DWDVQACGGT
HLPSTGLVGP IKILRTERIQ DGVERIIFAC GEAAIREWQK ERDLLKKASN VLRVPPEKLP
ETAERFFNEW KEARKEVDKL KKELARLLVY ELESKMQKIG SIEFIGEVVE GSMEDLRELV
EKLKKPKRVV VLISRDGYFA VSVGSEVGVE ANELAKKITL IAGGGGGGRR DIAQGKVKDI
SKAKDVIESI KSMFS
