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(-) Description

Title :  STRUCTURES OF ACTINONIN BOUND PEPTIDE DEFORMYLASES FROM E. FAECALIS AND S. PYOGENES
 
Authors :  E. E. Kim, K. -H. Kim, J. H. Moon, K. Choi, H. K. Lee, H. S. Park
Date :  05 Feb 07  (Deposition) - 04 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdf, Peptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. E. Kim, K. -H. Kim, J. H. Moon, K. Choi, H. K. Lee, H. S. Park
Structures Of Actinonin Bound Peptide Deformylases From E. Faecalis And S. Pyogenes
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF
    Mutation: YES
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Strain: ATCC 700802
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , CYS A:114 , HIS A:157 , HIS A:161 , HOH A:511BINDING SITE FOR RESIDUE NI A 400
2AC2SOFTWARESER A:102 , GLN A:104 , HOH A:717 , HOH A:761BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OS0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:24 -Pro A:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OS0)

(-) Exons   (0, 0)

(no "Exon" information available for 2OS0)

(-) 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:179
 aligned with DEF_ENTFA | Q82ZJ0 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:188
                                                                                                                                                                                                                    187 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      | 
            DEF_ENTFA     1 MITMKDIIREGNPTLRAVAEEVPVPITEEDRQLGEDMLTFLKNSQDPVKAEELQLRGGVGLAAPQLDISKRIIAVHVPSNDPENETPSLSTVMYNPKILSHSVQDVCLGEGEGCLSVDRDVPGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFYDHINKENPFALKEGVLVIE-   -
               SCOP domains d2os0a_ A: Peptide deformylase                                                                                                                                                               SCOP domains
               CATH domains 2os0A00 A:1-188 Peptide Deformylase                                                                                                                                                          CATH domains
               Pfam domains ---Pep_deformylase-2os0A01 A:4-177                                                                                                                                               ----------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee.---------.eeeeeeeeeeeee...eeee..................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2os0 A   1 MITMKDIIREGNPTLRAVAEEVPVPITEEDRQLGEDMLTFLKNSQDPVKAEELQLRGDVGLAAPQLDISKRIIAVHVP---------SLSTVMYNPKILSHSVQDVCLGEGEGCLSVDRDVPGYVVRHNKITVSYFDMAGEKHKVRLKNYEAIVVQHEIDHINGIMFYDHINKENPFALKEGVLVIEL 188
                                    10        20        30        40        50        60        70       | -       |90       100       110       120       130       140       150       160       170       180        
                                                                                                        78        88
   Legend:   → Mismatch (orange background)
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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) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pep_deformylase] (48)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEF_ENTFA | Q82ZJ0)
molecular function
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042586    peptide deformylase activity    Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
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.

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 Related Entries

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        DEF_ENTFA | Q82ZJ0: 2os1

(-) Related Entries Specified in the PDB File

2os1 2os3