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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL TYROSYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(TYR) AND L-TYROSINE
 
Authors :  T. Kobayashi, O. Nureki, R. Ishitani, M. Tukalo, S. Cusack, K. Sakamoto, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Dec 02  (Deposition) - 03 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Aminoacyl-Trna Synthetase, Ligase, Trna, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kobayashi, O. Nureki, R. Ishitani, A. Yaremchuk, M. Tukalo, S. Cusack, K. Sakamoto, S. Yokoyama
Structural Basis For Orthogonal Trna Specificities Of Tyrosyl-Trna Synthetases For Genetic Code Expansion
Nat. Struct. Biol. V. 10 425 2003
PubMed-ID: 12754495  |  Reference-DOI: 10.1038/NSB934
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA(TYR)
    Chains: B
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS IN METHANOCOCCUS JANNASCHII.
    Synthetic: YES
 
Molecule 2 - TYROSYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TYRS
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2TYR1Mod. Amino AcidTYROSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2TYR2Mod. Amino AcidTYROSINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:60 , HOH B:350 , A B:509 , G B:510 , U B:548BINDING SITE FOR RESIDUE MG B 1501
2AC2SOFTWAREHOH B:61 , HOH B:288 , HOH B:289 , HOH B:290 , HOH B:291 , HOH B:292BINDING SITE FOR RESIDUE MG B 1502
3AC3SOFTWAREHIS A:160 , HOH A:722 , HOH A:723BINDING SITE FOR RESIDUE MG A 503
4AC4SOFTWAREHOH B:18 , HOH B:77 , HOH B:278 , HOH B:359 , HOH B:360 , HOH B:361BINDING SITE FOR RESIDUE MG B 1503
5AC5SOFTWARETYR A:32 , GLY A:34 , GLU A:36 , LEU A:65 , ALA A:67 , HIS A:70 , TYR A:151 , GLN A:155 , ASP A:158 , GLN A:173 , HOH A:599 , HOH A:705BINDING SITE FOR RESIDUE TYR A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J1U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:15 -Ser A:16
2Tyr A:251 -Pro A:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J1U)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYY_METJA37-46  1A:37-46
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYY_METJA37-46  2A:37-46

(-) Exons   (0, 0)

(no "Exon" information available for 1J1U)

(-) Sequences/Alignments

Asymmetric 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:299
 aligned with SYY_METJA | Q57834 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      
            SYY_METJA     1 MDEFEMIKRNTSEIISEEELREVLKKDEKSAYIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNDIHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL 306
               SCOP domains d1j1ua_ A: Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1j1uA01 A:1-196 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                               1j1uA0       2 A:197-306 Tyrosyl-Transfer RNA Synthetase                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh...eeehhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee.........-------........hhhhhhhhhhhh.........hhhhhhhhhh....eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------AA_TRNA_LI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j1u A   1 MDEFEMIKRNTSEIISEEELREVLKKDEKSAYIGFEPSGKIHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEIRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNDIHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGE-------GNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILEPIRKRL 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 |     210       220       230       240       250       260       270       280       290       300      
                                                                                                                                                                                                                                   202     210                                                                                                


Chain B from PDB  Type:RNA  Length:74
                                                                                                          
                 1j1u B 501 CCGGCGGUAGUUCAGCCUGGUAGAACGGCGGACUGUAGAUCCGCAUGUCGCUGGUUCAAAUCCGGCCCGCCGGA 574
                                   510       520       530       540       550       560       570
   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  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J1U)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYY_METJA | Q57834)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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(+).
    GO:0004832    valine-tRNA ligase activity    Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + 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.
    GO:0006438    valyl-tRNA aminoacylation    The process of coupling valine to valyl-tRNA, catalyzed by valyl-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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYY_METJA | Q57834: 1u7d 1u7x 1zh0 1zh6 2ag6 2hgz 2pxh 2zp1 3d6u 3d6v 3n2y 3qe4 4hjr 4hjx 4hk4 4hpw 4nd6 4nd7 4nda 4nx2 4pbr 4pbs 4pbt 5u36

(-) Related Entries Specified in the PDB File

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