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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B (ATPDF1B)
 
Authors :  S. Fieulaine, T. Meinnel, C. Giglione
Date :  16 Mar 10  (Deposition) - 30 Mar 11  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Peptide Deformylase, 1B, Pdf, N-Terminal Excision Pathway, Nme, Arabidopsis Thaliana, Induced-Fit, Hydrolase, Metal-Binding, Mitochondrion, Protein Biosynthesis, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fieulaine, A. Boularot, I. Artaud, M. Desmadril, F. Dardel, T. Meinnel, C. Giglione
Trapping Conformational States Along Ligand-Binding Dynamic Of Peptide Deformylase: The Impact Of Induced Fit On Enzyme Catalysis
Plos Biol. V. 9 01066 2011
PubMed-ID: 21629676  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001066

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 1B
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: JM101TR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-193
    Gene: DEF
    Organism Common: THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PDF 1B, ATPDF1B, ATDEF2, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1ZN11Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:48 , CYS A:91 , HIS A:133 , HIS A:137 , ZN A:195 , HOH A:504BINDING SITE FOR RESIDUE ZN A 194
02AC2SOFTWAREGLN A:48 , GLU A:134 , ZN A:194 , HOH A:263 , HOH A:504BINDING SITE FOR RESIDUE ZN A 195
03AC3SOFTWAREASP A:40 , GLU A:63 , HOH A:226BINDING SITE FOR RESIDUE ZN A 196
04AC4SOFTWAREMET A:1 , GLU A:160 , GLU A:179 , GLU B:66BINDING SITE FOR RESIDUE ZN A 197
05AC5SOFTWAREASP A:30 , ASP A:34 , ZN A:199 , ASP B:30 , ASP B:34 , ZN B:198BINDING SITE FOR RESIDUE ZN A 198
06AC6SOFTWAREGLU A:69 , ZN A:198 , ASP B:30 , ASP B:34BINDING SITE FOR RESIDUE ZN A 199
07AC7SOFTWAREGLN B:48 , CYS B:91 , HIS B:133 , HIS B:137 , ZN B:195 , HOH B:505BINDING SITE FOR RESIDUE ZN B 194
08AC8SOFTWAREGLN B:48 , GLU B:134 , ZN B:194 , HOH B:236 , HOH B:505BINDING SITE FOR RESIDUE ZN B 195
09AC9SOFTWAREASP B:40 , GLU B:63 , HOH B:238 , HOH B:480BINDING SITE FOR RESIDUE ZN B 196
10BC1SOFTWAREGLU A:66 , MET B:1 , GLU B:160 , GLU B:179BINDING SITE FOR RESIDUE ZN B 197
11BC2SOFTWAREASP A:30 , ASP A:34 , ZN A:198 , GLU B:69BINDING SITE FOR RESIDUE ZN B 198

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M6O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:6 -Pro A:7
2Tyr B:6 -Pro B:7

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M6O)

(-) Exons   (0, 0)

(no "Exon" information available for 3M6O)

(-) Sequences/Alignments

Asymmetric 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:180
 aligned with DEF1B_ARATH | Q9FUZ2 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:180
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
          DEF1B_ARATH    81 LKIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEA 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh.........hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeee...........eeeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m6o A   1 MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEA 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with DEF1B_ARATH | Q9FUZ2 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:180
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
          DEF1B_ARATH    81 LKIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEA 260
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Pep_deformylase-3m6oB01 B:3-153                                                                                                                        --------------------------- Pfam domains (1)
           Pfam domains (2) --Pep_deformylase-3m6oB02 B:3-153                                                                                                                        --------------------------- Pfam domains (2)
         Sec.struct. author .......hhhhh.........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee...........eeeeeeeeeee...eeeeee.........eeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m6o B   1 MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEA 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (0, 0)

(no "SCOP Domain" information available for 3M6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M6O)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEF1B_ARATH | Q9FUZ2)
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:0031365    N-terminal protein amino acid modification    The alteration of the N-terminal amino acid residue in a protein.
    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: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

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UniProtKB/Swiss-Prot
        DEF1B_ARATH | Q9FUZ2: 3cpm 3m6p 3m6q 3m6r 3o3j 3pn2 3pn3 3pn4 3pn5 3pn6

(-) Related Entries Specified in the PDB File

3m6p ATPDF1B IN COMPLEX WITH ACTINONIN
3m6q ATPDF1B G41Q MUTANT IN COMPLEX WITH ACTINONIN
3m6r ATPDF1B G41M MUTANT IN COMPLEX WITH ACTINONIN