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(-) Description

Title :  PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES
 
Authors :  T. Meinnel, F. Dardel
Date :  15 Dec 97  (Deposition) - 18 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hydrolase, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Dardel, S. Ragusa, C. Lazennec, S. Blanquet, T. Meinnel
Solution Structure Of Nickel-Peptide Deformylase.
J. Mol. Biol. V. 280 501 1998
PubMed-ID: 9665852  |  Reference-DOI: 10.1006/JMBI.1998.1882
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: FMS (CODONS 1-147)
    Expression System Plasmid: PUC18 (IPTG-INDUCIBLE LAC PROMOTOR), PDEF-EC1-147
    Expression System Taxid: 562
    Fragment: ACTIVE CATALYTIC CORE, RESIDUES 1 - 147
    Gene: FMS (CODONS 1-147)
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: ACTIVE FORM CONTAINING ONE NICKEL ION IN THE METAL BINDING SITE
    Strain: PAL421TR

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:90 , HIS A:132 , HIS A:136BINDING SITE FOR RESIDUE NI A 148
2CATUNKNOWNCYS A:90 , HIS A:132 , HIS A:136CATALYTIC NICKEL ION.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ile A:8 -Pro A:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DEF)

(-) Sequences/Alignments

NMR Structure
   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:146
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:146
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142      
            DEF_ECOLI     3 VLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLS 148
               SCOP domains d2defa_ A: Peptide deformylase                                                                                                                     SCOP domains
               CATH domains 2defA00 A:2-147 Peptide Deformylase                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhhh....eee..........eeee.......eeee...eeeeee.......................eeeeee.......eeeee.hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2def A   2 VLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLS 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DEF)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (DEF_ECOLI | P0A6K3)
molecular function
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  2def
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_ECOLI | P0A6K3: 1bs4 1bs5 1bs6 1bs7 1bs8 1bsj 1bsk 1bsz 1def 1dff 1dtf 1g27 1g2a 1icj 1lru 1xem 1xen 1xeo 2ai8 2dtf 2kmn 2w3t 2w3u 3k6l 4al2 4al3 4az4 4v5b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DEF)