SYFB_PORGI
ID SYFB_PORGI Reviewed; 819 AA.
AC Q7MXR4;
DT 16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2003, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Phenylalanine--tRNA ligase beta subunit {ECO:0000255|HAMAP-Rule:MF_00283};
DE EC=6.1.1.20 {ECO:0000255|HAMAP-Rule:MF_00283};
DE AltName: Full=Phenylalanyl-tRNA synthetase beta subunit {ECO:0000255|HAMAP-Rule:MF_00283};
DE Short=PheRS {ECO:0000255|HAMAP-Rule:MF_00283};
GN Name=pheT {ECO:0000255|HAMAP-Rule:MF_00283}; OrderedLocusNames=PG_0099;
OS Porphyromonas gingivalis (strain ATCC BAA-308 / W83).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae;
OC Porphyromonas.
OX NCBI_TaxID=242619;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-308 / W83;
RX PubMed=12949112; DOI=10.1128/jb.185.18.5591-5601.2003;
RA Nelson K.E., Fleischmann R.D., DeBoy R.T., Paulsen I.T., Fouts D.E.,
RA Eisen J.A., Daugherty S.C., Dodson R.J., Durkin A.S., Gwinn M.L.,
RA Haft D.H., Kolonay J.F., Nelson W.C., Mason T.M., Tallon L., Gray J.,
RA Granger D., Tettelin H., Dong H., Galvin J.L., Duncan M.J., Dewhirst F.E.,
RA Fraser C.M.;
RT "Complete genome sequence of the oral pathogenic bacterium Porphyromonas
RT gingivalis strain W83.";
RL J. Bacteriol. 185:5591-5601(2003).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + H(+) +
CC L-phenylalanyl-tRNA(Phe); Xref=Rhea:RHEA:19413, Rhea:RHEA-COMP:9668,
CC Rhea:RHEA-COMP:9699, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:58095, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78531, ChEBI:CHEBI:456215; EC=6.1.1.20;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00283};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00283};
CC Note=Binds 2 magnesium ions per tetramer. {ECO:0000255|HAMAP-
CC Rule:MF_00283};
CC -!- SUBUNIT: Tetramer of two alpha and two beta subunits.
CC {ECO:0000255|HAMAP-Rule:MF_00283}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00283}.
CC -!- SIMILARITY: Belongs to the phenylalanyl-tRNA synthetase beta subunit
CC family. Type 1 subfamily. {ECO:0000255|HAMAP-Rule:MF_00283}.
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DR EMBL; AE015924; AAQ65345.1; -; Genomic_DNA.
DR RefSeq; WP_005873967.1; NC_002950.2.
DR PDB; 3ICA; X-ray; 2.44 A; A/B=503-712.
DR PDBsum; 3ICA; -.
DR AlphaFoldDB; Q7MXR4; -.
DR SMR; Q7MXR4; -.
DR STRING; 242619.PG_0099; -.
DR DNASU; 2551863; -.
DR EnsemblBacteria; AAQ65345; AAQ65345; PG_0099.
DR KEGG; pgi:PG_0099; -.
DR PATRIC; fig|242619.8.peg.90; -.
DR eggNOG; COG0072; Bacteria.
DR eggNOG; COG0073; Bacteria.
DR HOGENOM; CLU_016891_0_0_10; -.
DR OMA; ISYNWLK; -.
DR OrthoDB; 53568at2; -.
DR BioCyc; PGIN242619:G1G02-90-MON; -.
DR EvolutionaryTrace; Q7MXR4; -.
DR Proteomes; UP000000588; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004826; F:phenylalanine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006432; P:phenylalanyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd00769; PheRS_beta_core; 1.
DR CDD; cd02796; tRNA_bind_bactPheRS; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.70.380; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR Gene3D; 3.50.40.10; -; 1.
DR HAMAP; MF_00283; Phe_tRNA_synth_beta1; 1.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR005146; B3/B4_tRNA-bd.
DR InterPro; IPR009061; DNA-bd_dom_put_sf.
DR InterPro; IPR005121; Fdx_antiC-bd.
DR InterPro; IPR036690; Fdx_antiC-bd_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR045060; Phe-tRNA-ligase_IIc_bsu.
DR InterPro; IPR004532; Phe-tRNA-ligase_IIc_bsu_bact.
DR InterPro; IPR020825; Phe-tRNA_synthase-like_B3/B4.
DR InterPro; IPR041616; PheRS_beta_core.
DR InterPro; IPR002547; tRNA-bd_dom.
DR InterPro; IPR033714; tRNA_bind_bactPheRS.
DR InterPro; IPR005147; tRNA_synthase_B5-dom.
DR PANTHER; PTHR10947; PTHR10947; 1.
DR Pfam; PF03483; B3_4; 1.
DR Pfam; PF03484; B5; 1.
DR Pfam; PF03147; FDX-ACB; 1.
DR Pfam; PF01588; tRNA_bind; 1.
DR Pfam; PF17759; tRNA_synthFbeta; 1.
DR SMART; SM00873; B3_4; 1.
DR SMART; SM00874; B5; 1.
DR SMART; SM00896; FDX-ACB; 1.
DR SUPFAM; SSF46955; SSF46955; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF54991; SSF54991; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR TIGRFAMs; TIGR00472; pheT_bact; 1.
DR PROSITE; PS51483; B5; 1.
DR PROSITE; PS51447; FDX_ACB; 1.
DR PROSITE; PS50886; TRBD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Magnesium; Metal-binding; Nucleotide-binding; Protein biosynthesis;
KW Reference proteome; RNA-binding; tRNA-binding.
FT CHAIN 1..819
FT /note="Phenylalanine--tRNA ligase beta subunit"
FT /id="PRO_0000126927"
FT DOMAIN 42..154
FT /note="tRNA-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT DOMAIN 412..488
FT /note="B5"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT DOMAIN 726..819
FT /note="FDX-ACB"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT BINDING 466
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="shared with alpha subunit"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT BINDING 472
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="shared with alpha subunit"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT BINDING 475
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="shared with alpha subunit"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT BINDING 476
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="shared with alpha subunit"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00283"
FT HELIX 503..518
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 528..531
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 532..535
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 539..541
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 543..545
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 550..553
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 555..560
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 562..564
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 565..576
FT /evidence="ECO:0007829|PDB:3ICA"
FT TURN 577..579
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 581..595
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 607..621
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 636..649
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 654..656
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 657..661
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 667..675
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 680..687
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 689..694
FT /evidence="ECO:0007829|PDB:3ICA"
FT STRAND 701..707
FT /evidence="ECO:0007829|PDB:3ICA"
FT HELIX 708..711
FT /evidence="ECO:0007829|PDB:3ICA"
SQ SEQUENCE 819 AA; 91271 MW; 1CA333608A5794F0 CRC64;
MNISYKWLLE YLPCTLSPQE IADTLTSIGL ETGGVEEIET IRGGLRGLVI GHVLTCEEHP
NSDHLHITTV DVGADAPLQI VCGAPNVAAG QKVVVATVGT TLYHGEEEFA IKKSKIRGVE
SFGMICSEVE IGVGSSNDGT IVLPSDAPVG MPAAEYYHVE SDYCIEVDIT PNRVDATSHY
GVARDLAASL KRNGVPAELK LPEVNLPTDI IDSRIEVKVA DATACPRYQG LVIRDITVGE
SPEWLRNRLQ AIGLRPINNI VDITNYVLHE FGQPLHAFDL AFIKGDRVHV QTVAEGTPFV
TLDGVERKLT AEDLMICDSN GDPMCVAGVF GGLHSGVTEK TTDIFLESAN FNPTMVRRTA
RRLGLNTDSS FRFERGLDPE RTDWALRRAA SLILEIAGGH LGGMTDVYSN PLKPHLISLS
FEKVNSVIGR TIEPEMVRSI LNSLEIRISK EEDGVMTLEV PRYRTDVTRD VDVIEEIMRI
YGYNQVELTG YIRASLGHET ETDRRYKWQT VVSEQLVGAG FNEILNNSLT AGSYYEGLKS
HPREMAVELM NPLSQELNCM RQTLLFGGLE TLSHNLRRKH LSLYLFEWGK CYRFHAAKRT
DETPLAAYAE DDRLGIWICG QRVHNSWAHP EEPTSVFELK AVVEQVLCRV GIETGAYTLK
TADNDLYASA MEVKTRSGKL LGTFGTVSTE LIKRFEIEQP VYFAELLWDA LMSESARYKL
EARDLPRFPE VKRDLALLLD KAVSFAEIES LARGCEKKLL RRVELFDVYE GKNLPAGKKS
YAVSFFLRND EKTLNDKQIE AIMAKIRTTL EQKLGAQLR
