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(-) Description

Title :  STRUCTURAL BASIS OF YEAST AMINOACYL-TRNA SYNTHETASE COMPLEX FORMATION REVEALED BY CRYSTAL STRUCTURES OF TWO BINARY SUB-COMPLEXES
 
Authors :  H. Simader, C. Koehler, J. Basquin, D. Suck
Date :  22 Jul 06  (Deposition) - 05 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protein Complex Protein Interaction Gst-Fold, Ligase/Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Simader, M. Hothorn, C. Kohler, J. Basquin, G. Simos, D. Suck
Structural Basis Of Yeast Aminoacyl-Trna Synthetase Complex Formation Revealed By Crystal Structures Of Two Binary Sub-Complexes.
Nucleic Acids Res. V. 34 3968 2006
PubMed-ID: 16914447  |  Reference-DOI: 10.1093/NAR/GKL560
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE, CYTOPLASMIC
    Chains: A
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-DERIVATIVE
    Expression System Strain: BL21 DE3 STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-160
    Gene: MES1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: METHIONINE-TRNA LIGASE, METRS
 
Molecule 2 - GU4 NUCLEIC-BINDING PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM-DERIVATIVE
    Expression System Strain: BL21 DE3 STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-122
    Gene: ARC1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: G4P1 PROTEIN, P42, ARC1 PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2HSN)

(-) Sites  (0, 0)

(no "Site" information available for 2HSN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL105W1YGL105W.1VII:307440-3085701131ARC1_YEAST1-3763761B:3-122120
2.1YGR264C1YGR264C.1VII:1021859-10196042256SYMC_YEAST1-7517511A:3-162160

(-) 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:160
 aligned with SYMC_YEAST | P00958 from UniProtKB/Swiss-Prot  Length:751

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
           SYMC_YEAST     1 MSFLISFDKSKKHPAHLQLANNLKIALALEYASKNLKPEVDNDNAAMELRNTKEPFLLFDANAILRYVMDDFEGQTSDKYQFALASLQNLLYHKELPQQHVEVLTNKAIENYLVELKEPLTTTDLILFANVYALNSSLVHSKFPELPSKVHNAVALAKKH 160
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........hhhhhhhhhhhhhhhhhhh......ee........eee........hhhhhhhhhh.......hhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:3-162 UniProt: 1-751 [INCOMPLETE]                                                                                                               Transcript 2
                 2hsn A   3 MSFLISFDKSKKHPAHLQLANNLKIALALEYASKNLKPEVDNDNAAMELRNTKEPFLLFDANAILRYVMDDFEGQTSDKYQFALASLQNLLYHKELPQQHVEVLTNKAIENYLVELKEPLTTTDLILFANVYALNSSLVHSKFPELPSKVHNAVALAKKH 162
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with ARC1_YEAST | P46672 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
           ARC1_YEAST     1 MSDLVTKFESLIISKYPVSFTKEQSAQAAQWESVLKSGQIQPHLDQLNLVLRDNTFIVSTLYPTSTDVHVFEVALPLIKDLVASSKDVKSTYTTYRHILRWIDYMQNLLEVSSTDKLEIN 120
               SCOP domains d2hsnb_ B: GU4 nucleic-binding protein 1, Arc1p                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-122 UniProt: 1-376 [INCOMPLETE]                                                                       Transcript 1
                 2hsn B   3 MSDLVTKFESLIISKYPVSFTKEQSAQAAQWESVLKSGQIQPHLDQLNLVLRDNTFIVSTLYPTSTDVHVFEVALPLIKDLVASSKDVKSTYTTYRHILRWIDYMQNLLEVSSTDKLEIN 122
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HSN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HSN)

(-) Gene Ontology  (18, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYMC_YEAST | P00958)
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:0004825    methionine-tRNA ligase activity    Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
    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).
biological process
    GO:0006431    methionyl-tRNA aminoacylation    The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-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: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.
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:0017102    methionyl glutamyl tRNA synthetase complex    A complex consisting of methionyl- and glutamyl-tRNA synthetases. The tRNA synthetases present in the complex bind to their cognate tRNAs more efficiently than they do as monomers.

Chain B   (ARC1_YEAST | P46672)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0080025    phosphatidylinositol-3,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
    GO:0032266    phosphatidylinositol-3-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
    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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0051351    positive regulation of ligase activity    Any process that activates or increases the frequency, rate or extent of ligase activity, the catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage, usually in a nucleoside triphosphate.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0017102    methionyl glutamyl tRNA synthetase complex    A complex consisting of methionyl- and glutamyl-tRNA synthetases. The tRNA synthetases present in the complex bind to their cognate tRNAs more efficiently than they do as monomers.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARC1_YEAST | P46672: 2hqt 2hrk 2hsm 4r1j

(-) Related Entries Specified in the PDB File

2hqt ISOLATED ARC1P N-TERMINAL DOMAIN
2hrk ARC1P N-TERMINAL DOMAIN IN COMPLEX WITH GLURS N-TERMINAL DOMAIN, CRYO
2hsm ARC1P N-TERMINAL DOMAIN IN COMPLEX WITH GLURS N-TERMINAL DOMAIN, ROOM TEMPERARTURE