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(-) Description

Title :  CRYSTAL STRUCTURE OF A C-TERMINALLY TRUNCATED CYT-18 PROTEIN
 
Authors :  P. J. Paukstelis, R. Coon, L. Madabusi, J. Nowakowski, A. Monzingo, J. R A. M. Lambowitz
Date :  29 Nov 04  (Deposition) - 15 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Cyt-18, Tyrosyl Trna Synthetase, Trna Ligase, Group I Intron, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. J. Paukstelis, R. Coon, L. Madabusi, J. Nowakowski, A. Monzingo, J. Robertus, A. M. Lambowitz
A Tyrosyl-Trna Synthetase Adapted To Function In Group I Intron Splicing By Acquiring A New Rna Binding Surface.
Mol. Cell V. 17 417 2005
PubMed-ID: 15694342  |  Reference-DOI: 10.1016/J.MOLCEL.2004.12.026

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL
    ChainsX
    EC Number6.1.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPEX-602
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentNUCLEOTIDE-BINDING FOLD, ALPHA HELICAL DOMAIN
    GeneCYT-18
    Organism ScientificNEUROSPORA CRASSA
    Organism Taxid5141
    SynonymTYROSINE--TRNA LIGASE, TYRRS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit X
Biological Unit 1 (2x)X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TYR1Mod. Amino AcidTYROSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TYR2Mod. Amino AcidTYROSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR X:99 , GLY X:101 , ASP X:103 , LEU X:133 , ASP X:143 , TYR X:247 , GLN X:251 , ASP X:254 , GLN X:267 , GLN X:273 , HOH X:847BINDING SITE FOR RESIDUE TYR X 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y42)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y42)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYYM_NEUCR104-114  1X:104-114
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYYM_NEUCR104-114  2X:104-114

(-) Exons   (0, 0)

(no "Exon" information available for 1Y42)

(-) 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 X from PDB  Type:PROTEIN  Length:371
 aligned with SYYM_NEUCR | P12063 from UniProtKB/Swiss-Prot  Length:669

    Alignment length:383
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418   
           SYYM_NEUCR    39 PKYTAKINEAEENWQARAEAIKKGKKQNTWDLFEERGYVKDTAGTKEHIAELMRTRRIGAYVGIDPTAPSLHVGHLLPLMPLFWMYLEGYKAFTLIGGSTAKIGDPTGRLKSRDHLSSSDATMNMTKIHYQLKKLWENVDTQMRARGYEADWARKRGIVNNNHWWNKQPMLEVLRRVGHALRIGPMLSRDTVKNKMTQGDGVSFAEFTYPIMQGWDWFELFYQQGVQMQIGGSDQYGNIISGLEVVKAARESEPDPQERKYVTPKTALDECVGFTVPLLTDSSGAKFGKSAGNAIWLDPYQTSVFDFYGYFVRRSDQEVENLLKLFTFMPISEITKTMEEHIKDPSKRVAQHTLAREVVTLVHGKQEASAAEDQHRMMYTGQM 421
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1y42X01 X:39-316 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                1y42X02 X:317-419 Tyrosyl-Transfer RNA Synthetase                                                       - CATH domains
               Pfam domains ----------------------------------------------------tRNA-synt_1b-1y42X01 X:91-418                                                                                                                                                                                                                                                                                                           - - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh....ee.hhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhh.eeeeee............-----------hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeehhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhh.eeee...........................hhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------AA_TRNA_LIG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y42 X  39 PKYTAKINEAEENWQARAEAIKKGKKQNTWDLFEERGYVKDTAGTKEHIAELMRTRRIGAYVGIDPTAPSLHVGHLLPLMPLFWMYLEGYKAFTLIGGSTAKIGDPTG-----------DATMNMTKIHYQLKKLWENVDTQMRARGYEADWARKRGIVNNNHWWNKQPMLEVLRRVGHALRIGPMLSRDTVKNKMTQGDGVSFAEFTYPIMQGWDWFELFYQQGVQMQIGGSDQYGNIISGLEVVKAARESEPDPQERKYVTPKTALDECVGFTVPLLTDSSGAKFGKSAGNAIWLDPYQTSVFDFYGYFVRRSDQEVENLLKLFTFMPISEITKTMEEHIKDPSKRVAQHTLAREVVTLVHGKQEASAAEDQHRMMYTG-Y 701
                                    48        58        68        78        88        98       108       118       128       138       | -       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418| |
                                                                                                                                     146         158                                                                                                                                                                                                                                                                  419 |
                                                                                                                                                                                                                                                                                                                                                                                                                        701

   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  (0, 0)

(no "SCOP Domain" information available for 1Y42)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain X   (SYYM_NEUCR | P12063)
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:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0043039    tRNA aminoacylation    The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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        SYYM_NEUCR | P120632rkj 4ojm

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