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Protein

Proline--tRNA ligase

Gene

proS

Organism
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of proline to tRNA(Pro) in a two-step reaction: proline is first activated by ATP to form Pro-AMP and then transferred to the acceptor end of tRNA(Pro). Can inadvertently accommodate and process cysteine.1 Publication

Catalytic activityi

ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro).UniRule annotation1 Publication

Kineticsi

  1. KM=0.26 mM for proline (at 60 degrees Celsius)2 Publications
  2. KM=0.05 mM for cysteine (at 60 degrees Celsius)2 Publications
  3. KM=4.1 µM for tRNA(Pro) (at 50 degrees Celsius)2 Publications
  4. KM=2.2 µM for tRNA(Pro) (at 50 degrees Celsius in the presence of LeuRS)2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei117Proline1 Publication1
    Binding sitei119Proline1 Publication1
    Binding sitei148ATP1 Publication1
    Binding sitei148Proline1 Publication1
    Binding sitei150ATP1 Publication1
    Binding sitei232ATP1 Publication1
    Binding sitei235ATP1 Publication1
    Binding sitei237Proline1 Publication1
    Binding sitei269ATP1 Publication1
    Metal bindingi436Zinc; structural1 Publication1
    Metal bindingi441Zinc; structural1 Publication1
    Metal bindingi464Zinc; structural1 Publication1
    Metal bindingi467Zinc; structural1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Aminoacyl-tRNA synthetase, Ligase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    ATP-binding, Metal-binding, Nucleotide-binding, Zinc

    Enzyme and pathway databases

    SABIO-RKO26708.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Proline--tRNA ligaseUniRule annotationCurated (EC:6.1.1.15UniRule annotation1 Publication)
    Alternative name(s):
    Prolyl-tRNA synthetase1 PublicationUniRule annotation
    Short name:
    ProRS1 PublicationUniRule annotation
    Gene namesi
    Name:proS
    Ordered Locus Names:MTH_611
    OrganismiMethanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum)
    Taxonomic identifieri187420 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanobacteriaMethanobacterialesMethanobacteriaceaeMethanothermobacter
    Proteomesi
    • UP000005223 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001393521 – 482Proline--tRNA ligaseAdd BLAST482

    Interactioni

    Subunit structurei

    Homodimer. The dimer is functionally asymmetric: only one of the two active sites at a time is able to form prolyl-adenylate, and only one tRNA molecule binds per dimer. Interacts with LeuRS, which enhances tRNA(Pro) aminoacylation.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    leuSO275523EBI-7963357,EBI-7963108

    Protein-protein interaction databases

    IntActiO26708. 1 interactor.
    MINTiMINT-6664518.
    STRINGi187420.MTH611.

    Structurei

    Secondary structure

    1482
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi20 – 30Combined sources11
    Beta strandi33 – 35Combined sources3
    Helixi48 – 65Combined sources18
    Turni66 – 68Combined sources3
    Beta strandi76 – 79Combined sources4
    Helixi80 – 83Combined sources4
    Helixi87 – 92Combined sources6
    Turni93 – 96Combined sources4
    Beta strandi99 – 103Combined sources5
    Beta strandi106 – 114Combined sources9
    Beta strandi116 – 118Combined sources3
    Helixi119 – 129Combined sources11
    Turni133 – 135Combined sources3
    Beta strandi138 – 147Combined sources10
    Turni156 – 158Combined sources3
    Beta strandi161 – 175Combined sources15
    Helixi176 – 196Combined sources21
    Beta strandi202 – 205Combined sources4
    Turni208 – 210Combined sources3
    Beta strandi216 – 224Combined sources9
    Beta strandi230 – 240Combined sources11
    Helixi242 – 247Combined sources6
    Beta strandi250 – 252Combined sources3
    Beta strandi254 – 256Combined sources3
    Beta strandi258 – 260Combined sources3
    Beta strandi262 – 268Combined sources7
    Helixi271 – 279Combined sources9
    Beta strandi283 – 287Combined sources5
    Turni290 – 292Combined sources3
    Beta strandi296 – 301Combined sources6
    Beta strandi304 – 307Combined sources4
    Helixi308 – 323Combined sources16
    Turni324 – 326Combined sources3
    Beta strandi329 – 331Combined sources3
    Helixi338 – 347Combined sources10
    Beta strandi351 – 356Combined sources6
    Helixi358 – 361Combined sources4
    Turni362 – 364Combined sources3
    Beta strandi365 – 373Combined sources9
    Beta strandi376 – 380Combined sources5
    Turni381 – 383Combined sources3
    Helixi384 – 408Combined sources25
    Beta strandi411 – 413Combined sources3
    Helixi417 – 427Combined sources11
    Beta strandi429 – 435Combined sources7
    Helixi439 – 449Combined sources11
    Beta strandi452 – 458Combined sources7
    Turni465 – 467Combined sources3
    Beta strandi473 – 478Combined sources6

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1NJ1X-ray2.55A1-481[»]
    1NJ2X-ray3.11A1-481[»]
    1NJ5X-ray2.80A1-481[»]
    1NJ6X-ray2.85A1-481[»]
    ProteinModelPortaliO26708.
    SMRiO26708.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO26708.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni346 – 376Interaction with tRNABy similarityAdd BLAST31

    Domaini

    Consists of three domains: the N-terminal catalytic domain, the anticodon-binding domain and the C-terminal extension. The C-terminal extension binds a zinc ion, which probably plays a non-essential structural role in stabilizing the fold of C-terminal domain.

    Sequence similaritiesi

    Belongs to the class-II aminoacyl-tRNA synthetase family. ProS type 3 subfamily.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiarCOG00402. Archaea.
    COG0442. LUCA.
    KOiK01881.
    OMAiVYWGKAY.

    Family and domain databases

    CDDicd00778. ProRS_core_arch_euk. 1 hit.
    Gene3Di3.30.110.30. 1 hit.
    3.40.50.800. 1 hit.
    HAMAPiMF_01571. Pro_tRNA_synth_type3. 1 hit.
    InterProiIPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR002316. Pro-tRNA-ligase_IIa.
    IPR004499. Pro-tRNA-ligase_IIa_arc-type.
    IPR016061. Pro-tRNA_ligase_II_C.
    IPR017449. Pro-tRNA_synth_II.
    IPR033721. ProRS_core_arch_euk.
    [Graphical view]
    PANTHERiPTHR11451:SF6. PTHR11451:SF6. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF09180. ProRS-C_1. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01046. TRNASYNTHPRO.
    SMARTiSM00946. ProRS-C_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF52954. SSF52954. 1 hit.
    SSF64586. SSF64586. 1 hit.
    TIGRFAMsiTIGR00408. proS_fam_I. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O26708-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQKPIKKDPN RYHGEKMTEF SEWFHNILEE AEIIDQRYPV KGMHVWMPHG
    60 70 80 90 100
    FMIRKNTLKI LRRILDRDHE EVLFPLLVPE DELAKEAIHV KGFEDEVYWV
    110 120 130 140 150
    THGGLSKLQR KLALRPTSET VMYPMFALWV RSHTDLPMRF YQVVNTFRYE
    160 170 180 190 200
    TKHTRPLIRV REITTFKEAH TIHATASEAE EQVERAVEIY KEFFNSLGIP
    210 220 230 240 250
    YLITRRPPWD KFPGSEYTVA FDTLMPDGKT LQIGTVHNLG QTFARTFEIK
    260 270 280 290 300
    FETPEGDHEY VHQTCYGLSD RVIASVIAIH GDESGLCLPP DVAAHQVVIV
    310 320 330 340 350
    PIIFKKAAEE VMEACRELRS RLEAAGFRVH LDDRDIRAGR KYYEWEMRGV
    360 370 380 390 400
    PLRVEIGPRD LEKGAAVISR RDTGEKVTAD LQGIEETLRE LMKDILENLR
    410 420 430 440 450
    TRAWERMESE IREAETLEEA SRIVDEKRGI ISFMWCGEEE CGMDVEEKVR
    460 470 480
    VDILGIQEEG SGTCINCGRE APTGLTLPEH IS
    Length:482
    Mass (Da):55,806
    Last modified:January 1, 1998 - v1
    Checksum:i57D81ED7E9496BAA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000666 Genomic DNA. Translation: AAB85117.1.
    PIRiC69181.

    Genome annotation databases

    EnsemblBacteriaiAAB85117; AAB85117; MTH_611.
    KEGGimth:MTH_611.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000666 Genomic DNA. Translation: AAB85117.1.
    PIRiC69181.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1NJ1X-ray2.55A1-481[»]
    1NJ2X-ray3.11A1-481[»]
    1NJ5X-ray2.80A1-481[»]
    1NJ6X-ray2.85A1-481[»]
    ProteinModelPortaliO26708.
    SMRiO26708.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiO26708. 1 interactor.
    MINTiMINT-6664518.
    STRINGi187420.MTH611.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB85117; AAB85117; MTH_611.
    KEGGimth:MTH_611.

    Phylogenomic databases

    eggNOGiarCOG00402. Archaea.
    COG0442. LUCA.
    KOiK01881.
    OMAiVYWGKAY.

    Enzyme and pathway databases

    SABIO-RKO26708.

    Miscellaneous databases

    EvolutionaryTraceiO26708.

    Family and domain databases

    CDDicd00778. ProRS_core_arch_euk. 1 hit.
    Gene3Di3.30.110.30. 1 hit.
    3.40.50.800. 1 hit.
    HAMAPiMF_01571. Pro_tRNA_synth_type3. 1 hit.
    InterProiIPR002314. aa-tRNA-synt_IIb.
    IPR006195. aa-tRNA-synth_II.
    IPR004154. Anticodon-bd.
    IPR002316. Pro-tRNA-ligase_IIa.
    IPR004499. Pro-tRNA-ligase_IIa_arc-type.
    IPR016061. Pro-tRNA_ligase_II_C.
    IPR017449. Pro-tRNA_synth_II.
    IPR033721. ProRS_core_arch_euk.
    [Graphical view]
    PANTHERiPTHR11451:SF6. PTHR11451:SF6. 1 hit.
    PfamiPF03129. HGTP_anticodon. 1 hit.
    PF09180. ProRS-C_1. 1 hit.
    PF00587. tRNA-synt_2b. 1 hit.
    [Graphical view]
    PRINTSiPR01046. TRNASYNTHPRO.
    SMARTiSM00946. ProRS-C_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF52954. SSF52954. 1 hit.
    SSF64586. SSF64586. 1 hit.
    TIGRFAMsiTIGR00408. proS_fam_I. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSYP_METTH
    AccessioniPrimary (citable) accession number: O26708
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: January 1, 1998
    Last modified: November 2, 2016
    This is version 128 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Aminoacyl-tRNA synthetases
      List of aminoacyl-tRNA synthetase entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.