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(-) Description

Title :  SOLUTION STRUCTURE OF THE GGQ DOMAIN OF YAEJ PROTEIN FROM ESCHERICHIA COLI
 
Authors :  N. Nameki, M. Enomoto, H. Kogure, N. Tochio, P. Guntert
Date :  21 Sep 13  (Deposition) - 25 Dec 13  (Release) - 26 Mar 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Ggc Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kogure, Y. Handa, M. Nagata, N. Kanai, P. Guntert, K. Kubota, N. Nameki
Identification Of Residues Required For Stalled-Ribosome Rescue In The Codon-Independent Release Factor Yaej
Nucleic Acids Res. V. 42 3152 2014
PubMed-ID: 24322300  |  Reference-DOI: 10.1093/NAR/GKT1280

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE YAEJ
    Chains: A
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-110
    Gene: YAEJ, B0191, JW0187
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: PTH, ALTERNATIVE RIBOSOME-RESCUE FACTOR B

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2RTX)

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RF_PROK_IPS00745 Prokaryotic-type class I peptide chain release factors signature.ARFB_ECOLI21-37  1A:21-37
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RF_PROK_IPS00745 Prokaryotic-type class I peptide chain release factors signature.ARFB_ECOLI21-37  1A:21-37

(-) Exons   (0, 0)

(no "Exon" information available for 2RTX)

(-) Sequences/Alignments

NMR Structure
   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
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Chain A from PDB  Type:PROTEIN  Length:121
 aligned with ARFB_ECOLI | P40711 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
           ARFB_ECOLI     1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKARRPTRPTRASKERRLASK 122
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..ee......eeeee...............eeeeeee.hhh..hhhhhhhhhh.....ee...eeeeee.......hhhhhhhhhhhhhhhhhh..................-.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------RF_PROK_I        ------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rtx A   1 MIVISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHLISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTTEKKARRPTRSGPSSGEN-LYFQ 121
                                    10        20        30        40        50        60        70        80        90       100       110      |119  
                                                                                                                                              117 |   
                                                                                                                                                118
   Legend:   → Mismatch (orange background)
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  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 2RTX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (ARFB_ECOLI | P40711)
molecular function
    GO:0004045    aminoacyl-tRNA hydrolase activity    Catalysis of the reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003747    translation release factor activity    Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
    GO:0016150    translation release factor activity, codon nonspecific    A translation release factor that is not specific to particular codons; binds to guanine nucleotides.
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
biological process
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0072344    rescue of stalled ribosome    A process of translational elongation that takes place when a ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
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

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        ARFB_ECOLI | P40711: 4v95

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