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(-) Description

Title :  THE STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE (PDF) IN COMPLEX WITH PEPTIDOMIMETIC LIGAND BB2827
 
Authors :  R. K. Y. Cheng, L. Crawley, M. Wood, J. Barker, B. Felicetti, M. Whittaker
Date :  09 Oct 09  (Deposition) - 10 Nov 09  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ion Binding, Protein Biosynthesis, Translation, Iron, Metal- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Y. Cheng, L. Crawley, M. Wood, J. Barker, B. Felicetti, M. Whittaker
The Structure Of E. Coli Peptide Deformylase (Pdf) In Complex With Peptidomimetic Ligand Bb2827
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B, C
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF, FMS, B3287, JW3248
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
12BB2Ligand/Ion(2S,3R)-N~4~-[(1S)-1-(DIMETHYLCARBAMOYL)-2,2-DIMETHYLPROPYL]-N~1~,2-DIHYDROXY-3-(2-METHYLPROPYL)BUTANEDIAMIDE
2NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12BB1Ligand/Ion(2S,3R)-N~4~-[(1S)-1-(DIMETHYLCARBAMOYL)-2,2-DIMETHYLPROPYL]-N~1~,2-DIHYDROXY-3-(2-METHYLPROPYL)BUTANEDIAMIDE
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12BB1Ligand/Ion(2S,3R)-N~4~-[(1S)-1-(DIMETHYLCARBAMOYL)-2,2-DIMETHYLPROPYL]-N~1~,2-DIHYDROXY-3-(2-METHYLPROPYL)BUTANEDIAMIDE
2NI-1Ligand/IonNICKEL (II) ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
12BB-1Ligand/Ion(2S,3R)-N~4~-[(1S)-1-(DIMETHYLCARBAMOYL)-2,2-DIMETHYLPROPYL]-N~1~,2-DIHYDROXY-3-(2-METHYLPROPYL)BUTANEDIAMIDE
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:50 , CYS A:90 , HIS A:132 , HIS A:136 , 2BB A:170BINDING SITE FOR RESIDUE NI A 169
2AC2SOFTWAREGLU A:42 , GLY A:43 , ILE A:44 , GLY A:45 , GLN A:50 , ILE A:86 , GLY A:89 , CYS A:90 , LEU A:91 , ARG A:97 , CYS A:129 , HIS A:132 , GLU A:133 , HIS A:136 , NI A:169 , HOH A:249 , HOH A:264BINDING SITE FOR RESIDUE 2BB A 170
3AC3SOFTWAREGLN B:50 , CYS B:90 , HIS B:132 , HIS B:136 , 2BB B:170BINDING SITE FOR RESIDUE NI B 169
4AC4SOFTWAREGLU B:42 , GLY B:43 , ILE B:44 , GLY B:45 , GLN B:50 , ILE B:86 , GLU B:88 , GLY B:89 , CYS B:90 , LEU B:91 , CYS B:129 , HIS B:132 , GLU B:133 , HIS B:136 , NI B:169 , HOH B:263BINDING SITE FOR RESIDUE 2BB B 170
5AC5SOFTWAREGLN C:50 , CYS C:90 , HIS C:132 , HIS C:136 , HOH C:208BINDING SITE FOR RESIDUE NI C 169

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K6L)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:8 -Pro A:9
2Ile B:8 -Pro B:9
3Ile C:8 -Pro C:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K6L)

(-) Exons   (0, 0)

(no "Exon" information available for 3K6L)

(-) 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:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d3k6la_ A: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 3k6lA00 A:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhh....eee.hhhh....eeee.........eeeeeeeeeeee..eeeeeee..eeeeeeeeee..eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6l A   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d3k6lb_ B: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 3k6lB00 B:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhh....eee.hhhh....eeee.........eeeeeeeeeeee.....eeee..eeeeeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6l B   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:158
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152        
            DEF_ECOLI     3 VLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVE 160
               SCOP domains d3k6lc_ C: Peptide deformylase                                                                                                                                 SCOP domains
               CATH domains 3k6lC00 C:2-159 Peptide Deformylase                                                                                                                            CATH domains
           Pfam domains (1) Pep_deformylase-3k6lC01 C:2-152                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) Pep_deformylase-3k6lC02 C:2-152                                                                                                                        ------- Pfam domains (2)
           Pfam domains (3) Pep_deformylase-3k6lC03 C:2-152                                                                                                                        ------- Pfam domains (3)
         Sec.struct. author ........hhhhhh........hhhhhhhhhhhhhhhh.....eee.hhhh....eeee.-----...eeee...eeeeeeee..ee.........ee..eeeeeeeeee.....eeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k6l C   2 VLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVID-----DERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVE 159
                                    11        21        31        41        51        61     |  71        81        91       101       111       121       131       141       151        
                                                                                      61    67
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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 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 2def 2dtf 2kmn 2w3t 2w3u 4al2 4al3 4az4 4v5b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3K6L)