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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM ESCHERICHIA COLI IN COMPLEX WITH THE CCA-ACCEPTOR-T[PSI]C DOMAIN OF TRNA
 
Authors :  K. Ito, R. Murakami, M. Mochizuki, H. Qi, Y. Shimizu, K. I. Miura, T. Ueda T. Uchiumi
Date :  28 Oct 11  (Deposition) - 12 Sep 12  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Peptidyl-Trna Hydrolase, Cca-Acceptor-T[Psi]C Domain, Seven Beta- Strands Form, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ito, R. Murakami, M. Mochizuki, H. Qi, Y. Shimizu, K. Miura, T. Ueda, T. Uchiumi
Structural Basis For The Substrate Recognition And Catalysi Of Peptidyl-Trna Hydrolase.
Nucleic Acids Res. V. 40 10521 2012
PubMed-ID: 22923517  |  Reference-DOI: 10.1093/NAR/GKS790

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A, C
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PTH, B1204, JW1195
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: PTH
 
Molecule 2 - TRNA CCA-ACCEPTOR
    Chains: B, D
    Engineered: YES
    Other Details: RNA WAS REPEATED BY IN VITRO TRANSCRIPTION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3VJR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPT_TRNA_HYDROL_1PS01195 Peptidyl-tRNA hydrolase signature 1.PTH_ECOLI16-29
 		  2A:19-32
C:19-32
2PEPT_TRNA_HYDROL_2PS01196 Peptidyl-tRNA hydrolase signature 2.PTH_ECOLI110-120
 		  2A:113-123
C:113-123

(-) Exons   (0, 0)

(no "Exon" information available for 3VJR)

(-) 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:193
 aligned with PTH_ECOLI | P0A7D1 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
            PTH_ECOLI     2 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKAQ 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PEPT_TRNA_HYDR--------------------------------------------------------------------------------PEPT_TRNA_H-------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vjr A   5 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKAQ 197
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   


Chain B from PDB  Type:RNA  Length:36
                                                                    
                 3vjr B   1 GGGGGCUAAGCGGUUCGAUCCCGCUUAGCUCCACCA  36
                                    10        20        30      


Chain C from PDB  Type:PROTEIN  Length:193
 aligned with PTH_ECOLI | P0A7D1 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
            PTH_ECOLI     2 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKAQ 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhh.hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.hhh.eeeeeee.......eeeee......hhhhhhhhhhh......eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PEPT_TRNA_HYDR--------------------------------------------------------------------------------PEPT_TRNA_H-------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vjr C   5 TIKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLLVPTTFMNLSGKAVAAMASFFRINPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGLTKATNRLHAFKAQ 197
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   


Chain D from PDB  Type:RNA  Length:36
                                                                    
                 3vjr D   1 GGGGGCUAAGCGGUUCGAUCCCGCUUAGCUCCACCA  36
                                    10        20        30
   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 3VJR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (PTH_ECOLI | P0A7D1)
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:0006515    misfolded or incompletely synthesized protein catabolic process    The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PTH_ECOLI | P0A7D1: 2pth

(-) Related Entries Specified in the PDB File

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