SYP_THET8
ID SYP_THET8 Reviewed; 477 AA.
AC Q5SM28; Q93N97;
DT 05-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Proline--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_01571, ECO:0000305};
DE EC=6.1.1.15 {ECO:0000255|HAMAP-Rule:MF_01571, ECO:0000269|PubMed:12013438, ECO:0000269|PubMed:12130657};
DE AltName: Full=Prolyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_01571, ECO:0000303|PubMed:12130657};
DE Short=ProRS {ECO:0000255|HAMAP-Rule:MF_01571, ECO:0000303|PubMed:12130657};
GN Name=proS; OrderedLocusNames=TTHA0115;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Ahel I., Stathopoulos C., Hartsch T., Soell D.;
RT "Aminoacyl-tRNA formation in the hyperthermophile Thermus thermophilus.";
RL Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP PROLINE AND CYSTEINE ACTIVATION, FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12013438; DOI=10.1007/s007920100245;
RA Feng L., Stathopoulos C., Ahel I., Mitra A., Tumbula-Hansen D., Hartsch T.,
RA Soell D.;
RT "Aminoacyl-tRNA formation in the extreme thermophile Thermus
RT thermophilus.";
RL Extremophiles 6:167-174(2002).
RN [4]
RP PROLINE AND CYSTEINE ACTIVATION, FUNCTION, CATALYTIC ACTIVITY, AND KINETIC
RP PARAMETERS.
RX PubMed=12130657; DOI=10.1074/jbc.m206928200;
RA Ahel I., Stathopoulos C., Ambrogelly A., Sauerwald A., Toogood H.,
RA Hartsch T., Soell D.;
RT "Cysteine activation is an inherent in vitro property of prolyl-tRNA
RT synthetases.";
RL J. Biol. Chem. 277:34743-34748(2002).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.43 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP ZINC IONS AND TRNA, MUTAGENESIS OF TYR-477, AND SUBUNIT.
RX PubMed=10970866; DOI=10.1093/emboj/19.17.4745;
RA Yaremchuk A., Cusack S., Tukalo M.;
RT "Crystal structure of a eukaryote/archaeon-like prolyl-tRNA synthetase and
RT its complex with tRNAPro(CGG).";
RL EMBO J. 19:4745-4758(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH PROLINE; ZINC IONS,
RP TRNA AND PRO-AMP ANALOGS, AND SUBUNIT.
RX PubMed=11399074; DOI=10.1006/jmbi.2001.4712;
RA Yaremchuk A., Tukalo M., Groetli M., Cusack S.;
RT "A succession of substrate induced conformational changes ensures the amino
RT acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison
RT with histidyl-tRNA synthetase.";
RL J. Mol. Biol. 309:989-1002(2001).
CC -!- FUNCTION: Catalyzes the attachment of proline to tRNA(Pro) in a two-
CC step reaction: proline is first activated by ATP to form Pro-AMP and
CC then transferred to the acceptor end of tRNA(Pro). Can inadvertently
CC accommodate and process cysteine. {ECO:0000269|PubMed:12013438,
CC ECO:0000269|PubMed:12130657}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-
CC tRNA(Pro); Xref=Rhea:RHEA:14305, Rhea:RHEA-COMP:9700, Rhea:RHEA-
CC COMP:9702, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:60039,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78532, ChEBI:CHEBI:456215;
CC EC=6.1.1.15; Evidence={ECO:0000255|HAMAP-Rule:MF_01571,
CC ECO:0000269|PubMed:12013438, ECO:0000269|PubMed:12130657};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.15 mM for proline (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12130657};
CC KM=0.02 mM for cysteine (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12130657};
CC -!- SUBUNIT: Homodimer. Only one tRNA molecule binds per dimer.
CC {ECO:0000269|PubMed:10970866, ECO:0000269|PubMed:11399074}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01571}.
CC -!- DOMAIN: Consists of three domains: the N-terminal catalytic domain, the
CC anticodon-binding domain and the C-terminal extension. The C-terminal
CC extension binds a zinc ion, which probably plays a non-essential
CC structural role in stabilizing the fold of C-terminal domain.
CC -!- SIMILARITY: Belongs to the class-II aminoacyl-tRNA synthetase family.
CC ProS type 3 subfamily. {ECO:0000255|HAMAP-Rule:MF_01571, ECO:0000305}.
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DR EMBL; AF384553; AAK62359.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD69938.1; -; Genomic_DNA.
DR RefSeq; WP_011227720.1; NC_006461.1.
DR RefSeq; YP_143381.1; NC_006461.1.
DR PDB; 1H4Q; X-ray; 3.00 A; A/B=1-477.
DR PDB; 1H4S; X-ray; 2.85 A; A/B=1-477.
DR PDB; 1H4T; X-ray; 2.90 A; A/B/C/D=1-477.
DR PDB; 1HC7; X-ray; 2.43 A; A/B/C/D=1-477.
DR PDBsum; 1H4Q; -.
DR PDBsum; 1H4S; -.
DR PDBsum; 1H4T; -.
DR PDBsum; 1HC7; -.
DR AlphaFoldDB; Q5SM28; -.
DR SMR; Q5SM28; -.
DR STRING; 300852.55771497; -.
DR EnsemblBacteria; BAD69938; BAD69938; BAD69938.
DR GeneID; 3169620; -.
DR KEGG; ttj:TTHA0115; -.
DR PATRIC; fig|300852.9.peg.113; -.
DR eggNOG; COG0442; Bacteria.
DR HOGENOM; CLU_001882_4_2_0; -.
DR OMA; EVYWVTH; -.
DR PhylomeDB; Q5SM28; -.
DR BRENDA; 6.1.1.15; 2305.
DR SABIO-RK; Q5SM28; -.
DR EvolutionaryTrace; Q5SM28; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004827; F:proline-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006433; P:prolyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd00778; ProRS_core_arch_euk; 1.
DR Gene3D; 3.30.110.30; -; 1.
DR Gene3D; 3.30.930.10; -; 1.
DR Gene3D; 3.40.50.800; -; 1.
DR HAMAP; MF_01571; Pro_tRNA_synth_type3; 1.
DR InterPro; IPR002314; aa-tRNA-synt_IIb.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR004154; Anticodon-bd.
DR InterPro; IPR036621; Anticodon-bd_dom_sf.
DR InterPro; IPR002316; Pro-tRNA-ligase_IIa.
DR InterPro; IPR004499; Pro-tRNA-ligase_IIa_arc-type.
DR InterPro; IPR016061; Pro-tRNA_ligase_II_C.
DR InterPro; IPR017449; Pro-tRNA_synth_II.
DR InterPro; IPR033721; ProRS_core_arch_euk.
DR PANTHER; PTHR43382; PTHR43382; 1.
DR Pfam; PF03129; HGTP_anticodon; 1.
DR Pfam; PF09180; ProRS-C_1; 1.
DR Pfam; PF00587; tRNA-synt_2b; 1.
DR PRINTS; PR01046; TRNASYNTHPRO.
DR SMART; SM00946; ProRS-C_1; 1.
DR SUPFAM; SSF55681; SSF55681; 1.
DR SUPFAM; SSF64586; SSF64586; 1.
DR TIGRFAMs; TIGR00408; proS_fam_I; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 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; Zinc.
FT CHAIN 1..477
FT /note="Proline--tRNA ligase"
FT /id="PRO_0000248229"
FT REGION 340..369
FT /note="Interaction with tRNA"
FT BINDING 111
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000269|PubMed:11399074"
FT BINDING 113
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000269|PubMed:11399074"
FT BINDING 142
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:11399074"
FT BINDING 142
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000269|PubMed:11399074"
FT BINDING 153
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:11399074"
FT BINDING 225
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:11399074"
FT BINDING 228
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:11399074"
FT BINDING 230
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000269|PubMed:11399074"
FT BINDING 262
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:11399074"
FT BINDING 264
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:11399074"
FT BINDING 427
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:10970866,
FT ECO:0000269|PubMed:11399074"
FT BINDING 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:10970866,
FT ECO:0000269|PubMed:11399074"
FT BINDING 458
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:10970866,
FT ECO:0000269|PubMed:11399074"
FT BINDING 461
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:10970866,
FT ECO:0000269|PubMed:11399074"
FT MUTAGEN 477
FT /note="Y->A: Slightly reduces the aminoacylation activity."
FT /evidence="ECO:0000269|PubMed:10970866"
FT MUTAGEN 477
FT /note="Y->F: Little change in the aminoacylation activity."
FT /evidence="ECO:0000269|PubMed:10970866"
FT HELIX 10..24
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 41..60
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 81..87
FT /evidence="ECO:0007829|PDB:1H4S"
FT HELIX 88..90
FT /evidence="ECO:0007829|PDB:1H4S"
FT STRAND 92..108
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 113..123
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 132..141
FT /evidence="ECO:0007829|PDB:1HC7"
FT TURN 149..151
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 154..167
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 168..190
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 195..198
FT /evidence="ECO:0007829|PDB:1HC7"
FT TURN 201..203
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 208..217
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 223..233
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 235..239
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 251..253
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 255..262
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 264..273
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:1H4S"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 289..294
FT /evidence="ECO:0007829|PDB:1HC7"
FT TURN 298..300
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 301..317
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 328..330
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 332..341
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 345..350
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 352..356
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 359..364
FT /evidence="ECO:0007829|PDB:1HC7"
FT TURN 365..367
FT /evidence="ECO:0007829|PDB:1H4Q"
FT STRAND 371..373
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 374..376
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 377..402
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 404..406
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 410..416
FT /evidence="ECO:0007829|PDB:1HC7"
FT TURN 417..419
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 420..424
FT /evidence="ECO:0007829|PDB:1HC7"
FT HELIX 430..440
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 443..451
FT /evidence="ECO:0007829|PDB:1HC7"
FT TURN 459..461
FT /evidence="ECO:0007829|PDB:1HC7"
FT STRAND 471..474
FT /evidence="ECO:0007829|PDB:1HC7"
SQ SEQUENCE 477 AA; 54488 MW; 6AA477F1EC4D12F5 CRC64;
MAKEKGLTPQ SQDFSEWYLE VIQKAELADY GPVRGTIVVR PYGYAIWENI QQVLDRMFKE
TGHQNAYFPL FIPMSFLRKE AEHVEGFSPE LAVVTHAGGE ELEEPLAVRP TSETVIGYMW
SKWIRSWRDL PQLLNQWGNV VRWEMRTRPF LRTSEFLWQE GHTAHATREE AEEEVRRMLS
IYARLAREYA AIPVIEGLKT EKEKFAGAVY TTTIEALMKD GKALQAGTSH YLGENFARAF
DIKFQDRDLQ VKYVHTTSWG LSWRFIGAII MTHGDDRGLV LPPRLAPIQV VIVPIYKDES
RERVLEAAQG LRQALLAQGL RVHLDDRDQH TPGYKFHEWE LKGVPFRVEL GPKDLEGGQA
VLASRLGGKE TLPLAALPEA LPGKLDAFHE ELYRRALAFR EDHTRKVDTY EAFKEAVQEG
FALAFHCGDK ACERLIQEET TATTRCVPFE AEPEEGFCVR CGRPSAYGKR VVFAKAY
