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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI, I222 CRYSTAL FORM
 
Authors :  R. Lam, T. E. Mcgrath, V. Romanov, S. A. Gothe, S. R. Peddi, E. Razumova, R. S. Lipman, A. A. Branstrom, N. Y. Chirgadze
Date :  16 Aug 10  (Deposition) - 17 Aug 11  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Peptidyl-Trna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Lam, T. E. Mcgrath, V. Romanov, S. A. Gothe, S. R. Peddi, E. Razumova, R. S. Lipman, A. A. Branstrom, N. Y. Chirgadze
Crystal Structure Of Peptidyl-Trna Hydrolase From Escherichia Coli, I222 Crystal Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A, B, C
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3) CODONPLUS RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ECEG_00530, ECS1709, PTH
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 550677
    Strain: B354
    Synonym: PTH

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3OFV)

(-) Sites  (0, 0)

(no "Site" information available for 3OFV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OFV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OFV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OFV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OFV)

(-) Exons   (0, 0)

(no "Exon" information available for 3OFV)

(-) Sequences/Alignments

Asymmetric/Biological 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:190
 aligned with D6J9H8_ECOLX | D6J9H8 from UniProtKB/TrEMBL  Length:194

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
         D6J9H8_ECOLX     2 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAF 191
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofv A   1 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAF 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with D6J9H8_ECOLX | D6J9H8 from UniProtKB/TrEMBL  Length:194

    Alignment length:201
                                      1                                                                                                                                                                                              
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
         D6J9H8_ECOLX     - ----------MTIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAF 191
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofv B -10 SSGLVPRGSHVTIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAF 190
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 


Chain C from PDB  Type:PROTEIN  Length:190
 aligned with D6J9H8_ECOLX | D6J9H8 from UniProtKB/TrEMBL  Length:194

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
         D6J9H8_ECOLX     2 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAF 191
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ofv C   1 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAF 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3OFV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OFV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OFV)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (D6J9H8_ECOLX | D6J9H8)
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.
biological process
    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.

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