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(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS TRBP111: A STRUCTURE-SPECIFIC TRNA BINDING PROTEIN
 
Authors :  M. A. Swairjo, A. J. Morales, C. C. Wang, A. R. Ortiz, P. Schimmel
Date :  08 Jul 03  (Deposition) - 05 Aug 03  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oligonucleotide, Oligosaccharide-Binding Fold, Ob-Fold, Beta-Barrel, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Swairjo, A. J. Morales, C. C. Wang, A. R. Ortiz, P. Schimmel
Crystal Structure Of Trbp111: A Strcuture-Specific Trna-Binding Protein
Embo J. V. 19 6287 2000
PubMed-ID: 11101501  |  Reference-DOI: 10.1093/EMBOJ/19.23.6287
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE BETA SUBUNIT
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTSMG32
    Expression System StrainTG1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMETG
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1PYB)

(-) Sites  (0, 0)

(no "Site" information available for 1PYB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PYB)

(-) Exons   (0, 0)

(no "Exon" information available for 1PYB)

(-) 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:107
 aligned with O66738_AQUAE | O66738 from UniProtKB/TrEMBL  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
         O66738_AQUAE     5 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 111
               SCOP domains d1pyba_ A: Structure-specific tRNA-binding protein TRBP111                                                  SCOP domains
               CATH domains 1pybA00 A:5-111 Nucleic acid-binding proteins                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.eeeeeeeeee........eeeeeee..eeeeeee......hhhhhh..eeeee...............ee.eee....eeeeee.......ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1pyb A   5 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 111
                                    14        24        34        44        54        64        74        84        94       104       

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with O66738_AQUAE | O66738 from UniProtKB/TrEMBL  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
         O66738_AQUAE     5 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 111
               SCOP domains d1pybb_ B: Structure-specific tRNA-binding protein TRBP111                                                  SCOP domains
               CATH domains 1pybB00 B:205-311 Nucleic acid-binding proteins                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.eeeeeeeeee.........eeeeee..eeeeee.hhhhh.hhhhhh..eeeee......hhhhh....ee.eee....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1pyb B 205 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 311
                                   214       224       234       244       254       264       274       284       294       304       

Chain C from PDB  Type:PROTEIN  Length:107
 aligned with O66738_AQUAE | O66738 from UniProtKB/TrEMBL  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
         O66738_AQUAE     5 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 111
               SCOP domains d1pybc_ C: Structure-specific tRNA-binding protein TRBP111                                                  SCOP domains
               CATH domains 1pybC00 C:5-111 Nucleic acid-binding proteins                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.eeeeeeeeee........eeeeeee..eeeeeee......hhhhhh..eeeee...............ee.eee....eee..........ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1pyb C   5 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 111
                                    14        24        34        44        54        64        74        84        94       104       

Chain D from PDB  Type:PROTEIN  Length:107
 aligned with O66738_AQUAE | O66738 from UniProtKB/TrEMBL  Length:111

    Alignment length:107
                                    14        24        34        44        54        64        74        84        94       104       
         O66738_AQUAE     5 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 111
               SCOP domains d1pybd_ D: Structure-specific tRNA-binding protein TRBP111                                                  SCOP domains
               CATH domains 1pybD00 D:205-311 Nucleic acid-binding proteins                                                             CATH domains
           Pfam domains (1) ------------tRNA_bind-1pybD01 D:217-309                                                                  -- Pfam domains (1)
           Pfam domains (2) ------------tRNA_bind-1pybD02 D:217-309                                                                  -- Pfam domains (2)
           Pfam domains (3) ------------tRNA_bind-1pybD03 D:217-309                                                                  -- Pfam domains (3)
           Pfam domains (4) ------------tRNA_bind-1pybD04 D:217-309                                                                  -- Pfam domains (4)
         Sec.struct. author ....hhhhhhh.eeeeeeeee..........eeeeee..eeeeee.hhhhh.hhhhhh..eeeee...............ee.eee....eee...........ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1pyb D 205 ALIGIEDFLKVDLRVAKVLSAERVEGSEKLLKLTLSLGDEERTVVAGIAKYYTPEELVGKKIVIVANLKPRKIFGIESQGMILAASDGENLSVIVPDRDVKEGAKLS 311
                                   214       224       234       244       254       264       274       284       294       304       

   Legend:   → Mismatch (orange background)
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  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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O66738_AQUAE | O66738)
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: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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
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.
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 Specified in the PDB File

1pxf E.COLI TRBP111