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(-) Description

Title :  S.PNEUMONIAE PDF COMPLEXED WITH SB-543668
 
Authors :  K. J. Smith, C. M. Petit, K. Aubart, M. Smyth, E. Mcmanus, J. Jones, A. Fosberry, C. Lewis, M. Lonetto, S. B. Christensen
Date :  29 Jul 05  (Deposition) - 06 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Smith, C. M. Petit, K. Aubart, M. Smyth, E. Mcmanus, J. Jones, A. Fosberry, C. Lewis, M. Lonetto, S. B. Christensen
Structural Variation And Inhibitor Binding In Polypeptide Deformylase From Four Different Bacterial Species.
Protein Sci. V. 12 349 2003
PubMed-ID: 12538898  |  Reference-DOI: 10.1110/PS.0229303
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DEF
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: ATCC BAA-255-R6
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
2SB81Ligand/Ion2-(3-BENZOYLPHENOXY)ETHYL(HYDROXY)FORMAMIDE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:76 , CYS A:130 , HIS A:173 , HIS A:177 , SB8 A:501BINDING SITE FOR RESIDUE NI A 601
2AC2SOFTWARETHR A:34 , SER A:117 , ARG A:146 , HOH A:3031 , HOH A:3088 , HOH A:3141 , HOH A:3176BINDING SITE FOR RESIDUE SO4 A 3001
3AC3SOFTWAREVAL A:70 , GLY A:71 , GLN A:76 , LEU A:123 , GLY A:126 , GLU A:128 , GLY A:129 , CYS A:130 , LEU A:131 , TYR A:166 , VAL A:170 , HIS A:173 , GLU A:174 , HIS A:177 , NI A:601BINDING SITE FOR RESIDUE SB8 A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:35 -Pro A:36

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AIA)

(-) 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:192
 aligned with DEF_STRR6 | Q8DP79 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:202
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  
            DEF_STRR6     2 SAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE 203
               SCOP domains d2aiaa_ A: Peptide deformylase                                                                                                                                                                             SCOP domains
               CATH domains 2aiaA00 A:1-203 Peptide Deformylase                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh......hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee..----------...eeeeeeeeeeeee...eeee..................ee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh...........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aia A   1 SAIERISKAAHLIDMCDIIREGNPSLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPN----------AYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE 203
                                    10        20        30        40        50        60        70        80        90         -|      110       120     ||131       141       151       161       171       181       191       201  
                                                                                                                    90        101                      126|                                                                           
                                                                                                                                                        128
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEF_STRR6 | Q8DP79)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_STRR6 | Q8DP79: 2ai7 2aie 3svj 4eox

(-) Related Entries Specified in the PDB File

2ai7 2ai8 2ai9 2aie