SYP_METTH
ID SYP_METTH Reviewed; 482 AA.
AC O26708;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 155.
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: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=MTH_611;
OS Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
OS 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanothermobacter.
OX NCBI_TaxID=187420;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=9371463; DOI=10.1128/jb.179.22.7135-7155.1997;
RA Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J.,
RA Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D.,
RA Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R.,
RA Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D.,
RA Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A.,
RA Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J.,
RA Reeve J.N.;
RT "Complete genome sequence of Methanobacterium thermoautotrophicum deltaH:
RT functional analysis and comparative genomics.";
RL J. Bacteriol. 179:7135-7155(1997).
RN [2]
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 [3]
RP SUBUNIT.
RX PubMed=16226256; DOI=10.1016/j.febslet.2005.09.025;
RA Ambrogelly A., Kamtekar S., Stathopoulos C., Kennedy D., Soell D.;
RT "Asymmetric behavior of archaeal prolyl-tRNA synthetase.";
RL FEBS Lett. 579:6017-6022(2005).
RN [4]
RP INTERACTION WITH LEURS, AND KINETIC PARAMETERS.
RX PubMed=15917221; DOI=10.1074/jbc.m503539200;
RA Praetorius-Ibba M., Rogers T.E., Samson R., Kelman Z., Ibba M.;
RT "Association between Archaeal prolyl- and leucyl-tRNA synthetases enhances
RT tRNA(Pro) aminoacylation.";
RL J. Biol. Chem. 280:26099-26104(2005).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH
RP AMINOACYL-ADENYLATE ANALOGS AND ZINC IONS, AND SUBUNIT.
RX PubMed=12578991; DOI=10.1073/pnas.0437911100;
RA Kamtekar S., Kennedy W.D., Wang J., Stathopoulos C., Soell D., Steitz T.A.;
RT "The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA
RT synthetases.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:1673-1678(2003).
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: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:12130657};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.26 mM for proline (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12130657, ECO:0000269|PubMed:15917221};
CC KM=0.05 mM for cysteine (at 60 degrees Celsius)
CC {ECO:0000269|PubMed:12130657, ECO:0000269|PubMed:15917221};
CC KM=4.1 uM for tRNA(Pro) (at 50 degrees Celsius)
CC {ECO:0000269|PubMed:12130657, ECO:0000269|PubMed:15917221};
CC KM=2.2 uM for tRNA(Pro) (at 50 degrees Celsius in the presence of
CC LeuRS) {ECO:0000269|PubMed:12130657, ECO:0000269|PubMed:15917221};
CC -!- SUBUNIT: Homodimer. The dimer is functionally asymmetric: only one of
CC the two active sites at a time is able to form prolyl-adenylate, and
CC only one tRNA molecule binds per dimer. Interacts with LeuRS, which
CC enhances tRNA(Pro) aminoacylation. {ECO:0000269|PubMed:12578991,
CC ECO:0000269|PubMed:15917221, ECO:0000269|PubMed:16226256}.
CC -!- INTERACTION:
CC O26708; O27552: leuS; NbExp=3; IntAct=EBI-7963357, EBI-7963108;
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; AE000666; AAB85117.1; -; Genomic_DNA.
DR PIR; C69181; C69181.
DR PDB; 1NJ1; X-ray; 2.55 A; A=1-472.
DR PDB; 1NJ2; X-ray; 3.11 A; A=1-472.
DR PDB; 1NJ5; X-ray; 2.80 A; A=1-472.
DR PDB; 1NJ6; X-ray; 2.85 A; A=1-472.
DR PDBsum; 1NJ1; -.
DR PDBsum; 1NJ2; -.
DR PDBsum; 1NJ5; -.
DR PDBsum; 1NJ6; -.
DR AlphaFoldDB; O26708; -.
DR SMR; O26708; -.
DR IntAct; O26708; 1.
DR MINT; O26708; -.
DR STRING; 187420.MTH_611; -.
DR EnsemblBacteria; AAB85117; AAB85117; MTH_611.
DR KEGG; mth:MTH_611; -.
DR PATRIC; fig|187420.15.peg.592; -.
DR HOGENOM; CLU_001882_4_2_2; -.
DR OMA; EVYWVTH; -.
DR SABIO-RK; O26708; -.
DR EvolutionaryTrace; O26708; -.
DR Proteomes; UP000005223; 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..482
FT /note="Proline--tRNA ligase"
FT /id="PRO_0000139352"
FT REGION 346..376
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000250"
FT BINDING 117
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 119
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 148
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 148
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 150
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 232
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 235
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 237
FT /ligand="L-proline"
FT /ligand_id="ChEBI:CHEBI:60039"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 269
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:12578991"
FT BINDING 436
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:12578991"
FT BINDING 441
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:12578991"
FT BINDING 464
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:12578991"
FT BINDING 467
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="structural"
FT /evidence="ECO:0000269|PubMed:12578991"
FT HELIX 20..30
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:1NJ6"
FT HELIX 48..65
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 80..83
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 87..92
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 93..96
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 106..114
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 119..129
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 133..135
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 138..147
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 156..158
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 161..175
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 176..196
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 202..205
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 216..224
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 230..240
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 242..247
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 250..252
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 254..256
FT /evidence="ECO:0007829|PDB:1NJ5"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 262..268
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 271..279
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 283..287
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 290..292
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 296..301
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 308..323
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 324..326
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 329..331
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 338..347
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 351..356
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 358..361
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 362..364
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 365..373
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 376..380
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 381..383
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 384..408
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 411..413
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 417..427
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 429..435
FT /evidence="ECO:0007829|PDB:1NJ1"
FT HELIX 439..449
FT /evidence="ECO:0007829|PDB:1NJ1"
FT STRAND 452..458
FT /evidence="ECO:0007829|PDB:1NJ1"
FT TURN 465..467
FT /evidence="ECO:0007829|PDB:1NJ1"
SQ SEQUENCE 482 AA; 55806 MW; 57D81ED7E9496BAA CRC64;
MQKPIKKDPN RYHGEKMTEF SEWFHNILEE AEIIDQRYPV KGMHVWMPHG FMIRKNTLKI
LRRILDRDHE EVLFPLLVPE DELAKEAIHV KGFEDEVYWV THGGLSKLQR KLALRPTSET
VMYPMFALWV RSHTDLPMRF YQVVNTFRYE TKHTRPLIRV REITTFKEAH TIHATASEAE
EQVERAVEIY KEFFNSLGIP YLITRRPPWD KFPGSEYTVA FDTLMPDGKT LQIGTVHNLG
QTFARTFEIK FETPEGDHEY VHQTCYGLSD RVIASVIAIH GDESGLCLPP DVAAHQVVIV
PIIFKKAAEE VMEACRELRS RLEAAGFRVH LDDRDIRAGR KYYEWEMRGV PLRVEIGPRD
LEKGAAVISR RDTGEKVTAD LQGIEETLRE LMKDILENLR TRAWERMESE IREAETLEEA
SRIVDEKRGI ISFMWCGEEE CGMDVEEKVR VDILGIQEEG SGTCINCGRE APTGLTLPEH
IS
