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(-) Description

Title :  TYROSYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TYROSINOL
 
Authors :  S. Cusack, A. Yaremchuk, I. Kriklivyi, M. Tukalo
Date :  28 Aug 02  (Deposition) - 12 Sep 02  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Atp + L-Tyrosine + Trna(Tyr)- >Amp + Ppi + L-Tyrosyl-Trna(Ty Class I Aminoacyl-Trna Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yaremchuk, I. Kriklivyi, M. Tukalo, S. Cusack
Class I Tyrosyl-Trna Synthetase Has A Class Ii Mode Or Trna Recognition
Embo J. V. 21 3829 2002
PubMed-ID: 12110594  |  Reference-DOI: 10.1093/EMBOJ/CDF373

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET29B
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
    Synonym: TYROSINE--TRNA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2TYE2Ligand/Ion4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:358 , ARG B:429 , SER B:431BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREARG A:48 , HIS A:52 , SER A:234 , LYS A:235BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREARG B:48 , HIS B:52 , HIS B:55 , SER B:234 , LYS B:235BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREPRO A:263 , ARG A:267 , HOH A:2143 , HOH A:2144 , PRO B:263 , ARG B:267BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREARG A:256 , TYR A:342 , LYS A:347BINDING SITE FOR RESIDUE SO4 A 505
6AC6SOFTWARELYS A:41 , GLY A:43 , ASP A:45 , GLN A:179 , ASP A:182 , GLU A:191 , GLN A:197 , ASN A:200BINDING SITE FOR RESIDUE TYE A1433
7AC7SOFTWARELYS B:41 , GLY B:43 , GLN B:179 , ASP B:182 , GLU B:191 , GLN B:197BINDING SITE FOR RESIDUE TYE B1433

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H3F)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:23 -Pro A:24
2Val B:23 -Pro B:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H3F)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S4PS50889 S4 RNA-binding domain profile.SYY_THET2369-430
 		  2A:369-430
B:369-430

(-) Exons   (0, 0)

(no "Exon" information available for 1H3F)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:403
 aligned with SYY_THET2 | P83453 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:428
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        
            SYY_THET2     5 GHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD 432
               SCOP domains d1h3fa1 A:5-347 Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                                                            d1h3fa2 A:352-432 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain              SCOP domains
               CATH domains ---1h3fA01 A:8-223 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                   1h3fA02 A:224-340 Tyrosyl-Transfer RNA Synthetase                                                                    -------    1h3fA03 A:352-430                                                              -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeehhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhhh..eeeeee...---------------------hhhhhhhhhhhhh.........eeeeehhhhhh..hhhhhhhhhh..hhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.....eeeee............hhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..hhhhh.......hhhhhhhhhhhhhhh.----....eeeehhhhh...eeehhhhhhhh....hhhhhhhhhhh..eee..ee......eee....eeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S4  PDB: A:369-430 UniProt: 369-430                           -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3f A   5 GHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDF---------------------TRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAK----EEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD 432
                                    14        24        34        44        54        64        74    |    -         -      |104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344  |    354       364       374       384       394       404       414       424        
                                                                                                     79                   101                                                                                                                                                                                                                                                   347  352                                                                                


Chain B from PDB  Type:PROTEIN  Length:406
 aligned with SYY_THET2 | P83453 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:428
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        
            SYY_THET2     5 GHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMIGDPSGRSKTRPPLTLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD 432
               SCOP domains d1h3fb1 B:5-343 Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                                                             d1h3fb2 B:353-432 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain             SCOP domains
               CATH domains ---1h3fB01 B:8-223 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                   1h3fB02 B:224-340 Tyrosyl-Transfer RNA Synthetase                                                                    ---         1h3fB03 B:353-431                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeehhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhhh..eeeeeehhhhhh.-------------hhhhhhhhhhhhhhhhh.........eeeeehhhhhh..hhhhhhhhhh..hhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeeee............hhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.......hhhhhhh...hhhhh.......hhhhhhhhhhhh---------...eee.hhhhh...eeehhhhhhhh....hhhhhhhhhhh..eee..ee......eee....eeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S4  PDB: B:369-430 UniProt: 369-430                           -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h3f B   5 GHTPEEALALLKRGAEEIVPEEELLAKLKEGRPLTVKLGADPTRPDLHLGHAVVLRKMRQFQELGHKVVLIIGDFTGMI-------------TLEETRENAKTYVAQAGKILRQEPHLFELRYNSEWLEGLTFKEVVRLTSLMTVAQMLEREDFKKRYEAGIPISLHELLYPFAQAYDSVAIRADVEMGGTDQRFNLLVGREVQRAYGQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTEPPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKAGPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYD---------EIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRILQRGKDRFVRVRLSD 432
                                    14        24        34        44        54        64        74        |-         -  |    104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334        |-       354       364       374       384       394       404       414       424        
                                                                                                         83            97                                                                                                                                                                                                                                                   343       353
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H3F)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYY_THET2 | P83453)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004831    tyrosine-tRNA ligase activity    Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
biological process
    GO:0006418    tRNA aminoacylation for protein translation    The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006437    tyrosyl-tRNA aminoacylation    The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYY_THET2 | P83453: 1h3e

(-) Related Entries Specified in the PDB File

1h3e TYROSYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH WILD-TYPE TRNATYR(GUA) AND WITH ATP AND TYROSINOL