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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM FRANCISELLA TULARENSIS
 
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 :  08 Jun 10  (Deposition) - 15 Jun 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Peptidyl-Trna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Clarke, V. Romanov, R. Lam, S. A. Gothe, S. R. Peddi, E. B. Razumova R. S. Lipman, A. A. Branstrom, N. Y. Chirgadze
Structure Of Francisella Tularensis Peptidyl-Trna Hydrolase
Acta Crystallogr. , Sect. F V. 67 446 2011
PubMed-ID: 21505237  |  Reference-DOI: 10.1107/S174430911100515X

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A
    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
    Fragment: UNP RESIDUES 1-188
    Gene: FTT_0680C, PTH
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 119856
    Synonym: PTH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:101 , GLN A:158BINDING SITE FOR RESIDUE CL A 500
2AC2SOFTWAREPHE A:40 , SER A:42 , ASN A:49 , LYS A:108 , GLY A:109 , ASP A:129BINDING SITE FOR RESIDUE EDO A 510
3AC3SOFTWAREHIS A:22 , GLY A:114 , VAL A:146 , HOH A:214 , HOH A:216 , HOH A:218BINDING SITE FOR RESIDUE EDO A 511
4AC4SOFTWAREASP A:35 , ASN A:36 , HIS A:142 , ILE A:170BINDING SITE FOR RESIDUE EDO A 512
5AC5SOFTWARELYS A:5 , ASP A:56 , TYR A:57 , TYR A:83 , PRO A:140 , LYS A:145BINDING SITE FOR RESIDUE EDO A 513
6AC6SOFTWAREASN A:43 , PRO A:44 , LYS A:45BINDING SITE FOR RESIDUE EDO A 514

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPT_TRNA_HYDROL_2PS01196 Peptidyl-tRNA hydrolase signature 2.PTH_FRATT111-121  1A:111-121

(-) Exons   (0, 0)

(no "Exon" information available for 3NEA)

(-) 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:187
 aligned with PTH_FRATT | Q5NGZ6 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
            PTH_FRATT     2 PKIKMIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVVLVFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSINQHLGTNDYLRLRIGIGHPGHKSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYKLEPVMQKL 188
               SCOP domains d3neaa_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Pept_tRNA_hydro-3neaA01 A:6-188                                                                                                                                                         Pfam domains
         Sec.struct. author ....eeee..........hhhhhhhhhhhhhhhhh....eeehhh.eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.hhh.eeeeeee.......eeeee......hhhhhhhhhhhh....eeeeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------PEPT_TRNA_H------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nea A   2 PKIKMIIGLGNIGKEYQDTRHNVGEWFIAKIAQDNNQSFSSNPKLNCNLAKVSIDYNNVVLVFPTTYMNNSGLAVSKVANFYKIAPAEILVVHDELDIDSGEIRLKKGGGHGGHNGLRSINQHLGTNDYLRLRIGIGHPGHKSKVANYVLSNPSIAQKKDIDSAIDNGICFLDDIINYKLEPVMQKL 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pept_tRNA_hydro] (10)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTH_FRATT | Q5NGZ6)
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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