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(-) Description

Title :  PLANT PEPTIDE DEFORMYLASE PDF1B CRYSTAL STRUCTURE
 
Authors :  D. W. Rodgers, R. L. Houtz, L. M. A. Dirk, J. J. Schmidt, Y. Cai
Date :  31 Mar 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha Beta, Chloroplast, Hydrolase, Iron, Metal-Binding, Protein Biosynthesis, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Dirk, J. J. Schmidt, Y. Cai, J. C. Barnes, K. M. Hanger, N. R. Nayak, M. A. Williams, R. B. Grossman, R. L. Houtz, D. W. Rodgers
Insights Into The Substrate Specificity Of Plant Peptide Deformylase, An Essential Enzyme With Potential For The Development Of Novel Biotechnology Applications In Agriculture
Biochem. J. V. 413 417 2008
PubMed-ID: 18412546  |  Reference-DOI: 10.1042/BJ20071641

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE, CHLOROPLAST
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 65-257
    Gene: PDF1B
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , ASN A:154 , GLY A:176 , TYR A:178 , ARG A:192 , ARG A:198BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREGLN A:128 , CYS A:171 , HIS A:213 , HIS A:217 , HOH A:293BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREGLU A:103 , LYS A:106 , ASP A:110 , ASP A:114BINDING SITE FOR RESIDUE ZN A 3
4AC4SOFTWAREASP A:74 , ASP A:99 , GLU A:238BINDING SITE FOR RESIDUE ZN A 4
5AC5SOFTWAREGLU A:237 , GLU A:240 , HOH A:272BINDING SITE FOR RESIDUE ZN A 5

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CPM)

(-) 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:184
 aligned with DEF1B_ARATH | Q9FUZ2 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:184
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253    
          DEF1B_ARATH    74 DVQFETPLKIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPER 257
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cpmA00 A:74-257 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh.........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee...........eeeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cpm A  74 DVQFETPLKIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPER 257
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
   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 3CPM)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CPM)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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        DEF1B_ARATH | Q9FUZ2: 3m6o 3m6p 3m6q 3m6r 3o3j 3pn2 3pn3 3pn4 3pn5 3pn6

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