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(-) Description

Title :  X-RAY STRUCTURE OF PEPTIDE DEFORMYLASE FROM ARABIDOPSIS THALIANA (ATPDF1A) IN COMPLEX WITH MET-ALA-SER
 
Authors :  S. Fieulaine, C. Juillan-Binard, A. Serero, F. Dardel, C. Giglione, T. Meinnel, J. -L. Ferrer
Date :  09 Jun 05  (Deposition) - 27 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Peptide Deformylase; Pdf1A; Eukaryote; Higher Plant; Arabidopsis Thaliana; Zinc Ion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fieulaine, C. Juillan-Binard, A. Serero, F. Dardel, C. Giglione, T. Meinnel, J. -L. Ferrer
The Crystal Structure Of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines For The Design Of Inhibitors Specific For The Bacterial Forms
J. Biol. Chem. V. 280 42315 2005
PubMed-ID: 16192279  |  Reference-DOI: 10.1074/JBC.M507155200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PQE30 DERIVATIVE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MATURE PROTEIN
    Gene: PDF1A
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PDF;
POLYPEPTIDE DEFORMYLASE
 
Molecule 2 - TRIPEPTIDE FRAGMENT
    Chains: D, E
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:54 , CYS A:111 , HIS A:153 , HIS A:157 , HOH A:199 , HOH D:4BINDING SITE FOR RESIDUE ZN A 198
2AC2SOFTWAREGLN B:54 , CYS B:111 , HIS B:153 , HIS B:157 , HOH B:199BINDING SITE FOR RESIDUE ZN B 198

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZY1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZY1)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZY1)

(-) 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 DEF1A_ARATH | Q9FV53 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:191
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 
          DEF1A_ARATH    79 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGPQ 269
               SCOP domains d1zy1a_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 1zy1A00 A:2-192 Peptide Deformylase                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee........hhhhhhhh....eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhh.....ee.hhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy1 A   2 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSH 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with DEF1A_ARATH | Q9FV53 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:191
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 
          DEF1A_ARATH    79 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGPQ 269
               SCOP domains d1zy1b_ B: automated matches                                                                                                                                                                    SCOP domains
               CATH domains 1zy1B00 B:2-192 Peptide Deformylase                                                                                                                                                             CATH domains
           Pfam domains (1) -Pep_deformylase-1zy1B01 B:3-173                                                                                                                                            ------------------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1zy1B02 B:3-173                                                                                                                                            ------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhhh.hhhhhhhh....eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhh.....ee.hhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy1 B   2 DLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSH 192
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 


Chain D from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 1zy1 D   1 MAS   3


Chain E from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 1zy1 E   1 MAS   3
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEF1A_ARATH | Q9FV53)
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:0043686    co-translational protein modification    The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
    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:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0009505    plant-type cell wall    A more or less rigid stucture lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF1A_ARATH | Q9FV53: 1zxz 1zy0 4je6 4je7 4je8

(-) Related Entries Specified in the PDB File

1zxz 1zy0