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(-) Description

Title :  CRYSTAL STRUCTURE OF PARTIALLY FOLDED INTERMEDIATE STATE OF PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  A. Kumar, N. Singh, R. Yadav, S. Sharma, A. Arora, T. P. Singh
Date :  04 Nov 09  (Deposition) - 10 Nov 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Synthesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, N. Singh, R. Yadav, S. Sharma, A. Arora, T. P. Singh
Structures Of Fully-Folded Native And Partially-Folded Intermediate States Of Peptidyl-Trna Hydrolase From Mycobacterium Smegmatis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDYL-TRNA HYDROLASE
    Chains: A
    EC Number: 3.1.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155
    Synonym: PTH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2EDO4Ligand/Ion1,2-ETHANEDIOL
3IPA3Ligand/IonISOPROPYL ALCOHOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:143BINDING SITE FOR RESIDUE IPA A 192
2AC2SOFTWAREGLU A:152 , HOH A:257BINDING SITE FOR RESIDUE IPA A 193
3AC3SOFTWAREILE A:177 , HOH A:360 , EDO A:6076BINDING SITE FOR RESIDUE IPA A 194
4AC4SOFTWAREASP A:95 , LEU A:97 , HIS A:115BINDING SITE FOR RESIDUE EDO A 6073
5AC5SOFTWAREGLY A:53 , HOH A:318 , HOH A:343 , EDO A:6075BINDING SITE FOR RESIDUE EDO A 6074
6AC6SOFTWAREEDO A:6074BINDING SITE FOR RESIDUE EDO A 6075
7AC7SOFTWARELYS A:44 , LYS A:45 , IPA A:194BINDING SITE FOR RESIDUE EDO A 6076
8AC8SOFTWAREPRO A:13 , SER A:68BINDING SITE FOR RESIDUE PEG A 6070
9AC9SOFTWARELYS A:107 , GLY A:111 , ARG A:132 , ARG A:134BINDING SITE FOR RESIDUE BME A 2053

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KK0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KK0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KK0)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPT_TRNA_HYDROL_1PS01195 Peptidyl-tRNA hydrolase signature 1.PTH_MYCS217-30  1A:17-30
2PEPT_TRNA_HYDROL_2PS01196 Peptidyl-tRNA hydrolase signature 2.PTH_MYCS2111-121  1A:111-121

(-) Exons   (0, 0)

(no "Exon" information available for 3KK0)

(-) 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:191
 aligned with PTH_MYCS2 | A0R3D3 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
            PTH_MYCS2     1 MAEPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIGSAFKVHKKSGAEVVTGRLAGTSVVLAKPRCYMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRLKLGGGEGGHNGLRSVASALGTKNFHRVRIGVGRPPGRKDPAAFVLENFTAAERAEVPTIVEQAADATELLIAQGLEPAQNTVHAW 191
               SCOP domains d3kk0a_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Pept_tRNA_hydro-3kk0A01 A:6-189                                                                                                                                                         -- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhhh.....ee......eeeeeee..eeeeeee...hhhhh..hhhhhhhhh..hhh.eeeeeee.......eeeee......hhhhhhhhhhhh....eeeeee........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PEPT_TRNA_HYDR--------------------------------------------------------------------------------PEPT_TRNA_H---------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kk0 A   1 MAEPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIGSAFKVHKKSGAEVVTGRLAGTTVVLAKPRISMNESGRQVGPLAKFYSVPPQQIVVIHDELDIDFGRIRLKLGGGEGGHNGLRSVASALGTKNFHRVRIGVGRPPGRKDPAAFVLENFTSAERAEVPTIVEQAADATELLIAQGLEPAQNTVHAW 191
                                    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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KK0)

(-) 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_MYCS2 | A0R3D3)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PTH_MYCS2 | A0R3D3: 2lgj 2naf 3kjz 3p2j

(-) Related Entries Specified in the PDB File

2z2k CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM TUBERCULOSIS
3kjz NATIVE PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM SMEGMATIS