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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF YEAST TYROSYL-TRNA SYNTHETASE
 
Authors :  M. Tsunoda, Y. Kusakabe, N. Tanaka, K. T. Nakamura
Date :  18 Apr 06  (Deposition) - 12 Jun 07  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  X,Y
Biol. Unit 1:  X,Y  (2x)
Keywords :  Tyrrs, Trna, Ligase-Trna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Tsunoda, Y. Kusakabe, N. Tanaka, S. Ohno, M. Nakamura, T. Senda, T. Moriguchi, N. Asai, M. Sekine, T. Yokogawa, K. Nishikawa, K. T. Nakamura
Structural Basis For Recognition Of Cognate Trna By Tyrosyl-Trna Synthetase From Three Kingdoms.
Nucleic Acids Res. V. 35 4289 2007
PubMed-ID: 17576676  |  Reference-DOI: 10.1093/NAR/GKM417

(-) Compounds

Molecule 1 - T-RNA (76-MER)
    Chains: Y
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TYROSYL-TRNA SYNTHETASE, CYTOPLASMIC
    Chains: X
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: TYROSYL-TRNA LIGASE, TYRRS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 12)

Asymmetric Unit (10, 12)
No.NameCountTypeFull Name
11MA1Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
22MG1Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
35MC1Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
45MU1Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
56IA1Mod. NucleotideN6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE
6M2G1Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
7MG1Ligand/IonMAGNESIUM ION
8OMG1Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
9PSU3Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
10YMP1Ligand/IonO-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE
Biological Unit 1 (9, 22)
No.NameCountTypeFull Name
11MA2Mod. Nucleotide6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE
22MG2Mod. Nucleotide2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
35MC2Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
45MU2Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
56IA2Mod. NucleotideN6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE
6M2G2Mod. NucleotideN2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
7MG-1Ligand/IonMAGNESIUM ION
8OMG2Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
9PSU6Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE
10YMP2Ligand/IonO-(ADENOSINE-5'-O-YL)-N-(L-TYROSYL)PHOSPHORAMIDATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA X:47 , THR X:49 , TYR X:56 , TYR X:101 , YMP X:601BINDING SITE FOR RESIDUE MG X 801
2AC2SOFTWARETYR X:43 , TRP X:44 , GLY X:45 , THR X:46 , ALA X:47 , HIS X:53 , GLY X:55 , TYR X:56 , LEU X:76 , ALA X:78 , HIS X:81 , VAL X:156 , TYR X:170 , GLN X:174 , ASP X:177 , GLN X:186 , GLY X:188 , GLY X:189 , ASP X:191 , GLN X:192 , ASN X:216 , PRO X:217 , MET X:218 , VAL X:219 , MG X:801 , HOH X:821 , HOH X:834BINDING SITE FOR RESIDUE YMP X 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DLC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DLC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DLC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DLC)

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGR185C1YGR185C.1VII:867525-8663411185SYYC_YEAST1-3943941X:8-356 (gaps)349

(-) 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:339
 aligned with SYYC_YEAST | P36421 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347         
           SYYC_YEAST     8 DPNEAFGLITKNLQEVLNPQIIKDVLEVQKRHLKLYWGTAPTGRPHCGYFVPMTKLADFLKAGCEVTVLLADLHAFLDNMKAPLEVVNYRAKYYELTIKAILRSINVPIEKLKFVVGSSYQLTPDYTMDIFRLSNIVSQNDAKRAGADVVKQVANPLLSGLIYPLMQALDEQFLDVDCQFGGVDQRKIFVLAEENLPSLGYKKRAHLMNPMVPGLAQGGKMSASDPNSKIDLLEEPKQVKKKINSAFCSPGNVEENGLLSFVQYVIAPIQELKFGTNHFEFFIDRPEKFGGPITYKSFEEMKLAFKEEKLSPPDLKIGVADAINELLEPIRQEFANNKEFQEASEKGYP 356
               SCOP domains d2dlcx_ X: automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2dlcX01 X:8-217 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                             ---2dl          cX02 X:221-356 Tyrosyl-Transfer RNA Synthetase                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...eeehhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhh...........hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeeee.......----------........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh........eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: X:8-356 (gaps) UniProt: 1-394 [INCOMPLETE]                                                                                                                                                                                                                                                                                                     Transcript 1
                 2dlc X   8 DPNEAFGLITKNLQEVLNPQIIKDVLEVQKRHLKLYWGTAPTGRPHCGYFVPMTKLADFLKAGCEVTVLLADLHAFLDNMKAPLEVVNYRAKYYELTIKAILRSINVPIEKLKFVVGSSYQLTPDYTMDIFRLSNIVSQNDAKRAGADVVKQVANPLLSGLIYPLMQALDEQFLDVDCQFGGVDQRKIFVLAEENLPSLGYKKRAHLMNPMVPGLA----------NSKIDLLEEPKQVKKKINSAFCSPGNVEENGLLSFVQYVIAPIQELKFGTNHFEFFIDRPEKFGGPITYKSFEEMKLAFKEEKLSPPDLKIGVADAINELLEPIRQEFANNKEFQEASEKGYP 356
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217     |   -      |237       247       257       267       277       287       297       307       317       327       337       347         
                                                                                                                                                                                                                                                 223        234                                                                                                                          


Chain Y from PDB  Type:DNA/RNA  Length:74
                                                                                                          
                 2dlc Y 501 CUCUCGGUAgCCAAGUgGGAAGGCgCAAGAUGuAaAuCUUGAGGUcGGGCGuuCGaCUCGCCCCCGGGAGACCA 576
                                   510     ||521    |  531| | | |542     | 552 ||  | 562       572    
                                   510-2MG16|     526-M2G1| | | |      548-5MC ||  |                  
                                          518-OMG       533 | | |            554-5MU                  
                                                          535-PSU             555-PSU                 
                                                            537-6IA              558-1MA              
                                                              539-PSU
   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 2DLC)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain X   (SYYC_YEAST | P36421)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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