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(-) Description

Title :  STREP PEPTIDE DEFORMYLASE WITH A TIME DEPENDENT DICHLOROBENZAMIDE-REVERSE HYDROXAMIC ACID
 
Authors :  N. Campobasso, K. J. Smith
Date :  13 Jul 11  (Deposition) - 27 Jul 11  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  P
Keywords :  Alpha-Beta, Peptide Deformylase, Metal Binding Protein, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Totoritis, C. Duraiswami, A. N. Taylor, J. J. Kerrigan, N. Campobasso, K. J. Smith, P. Ward, B. W. King, M. Murrayz-Thompson, A. D. Jones, G. S. Van Aller, K. M. Aubart, M. Zalacain, S. H. Thrall, T. D. Meek, B. Schwartz
Understanding The Origins Of Time-Dependent Inhibition By Polypeptide Deformylase Inhibitors.
Biochemistry V. 50 6642 2011
PubMed-ID: 21711014  |  Reference-DOI: 10.1021/BI200655G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 3
    Chains: P
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DEFB, DEF3
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: PDF 3, POLYPEPTIDE DEFORMYLASE 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
15LI1Ligand/Ion2,3-DICHLORO-N-{2-[FORMYL(HYDROXY)AMINO]ETHYL}BENZAMIDE
2NI1Ligand/IonNICKEL (II) ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN P:77 , CYS P:130 , HIS P:173 , HIS P:177 , 5LI P:205BINDING SITE FOR RESIDUE NI P 204
2AC2SOFTWARETHR P:35 , SER P:118 , ARG P:146 , HOH P:237 , HOH P:343 , HOH P:371BINDING SITE FOR RESIDUE SO4 P 3001
3AC3SOFTWAREGLY P:70 , VAL P:71 , GLY P:72 , GLN P:77 , LEU P:124 , GLU P:128 , GLY P:129 , CYS P:130 , LEU P:131 , ILE P:169 , VAL P:170 , HIS P:173 , GLU P:174 , HIS P:177 , NI P:204BINDING SITE FOR RESIDUE 5LI P 205
4AC4SOFTWAREALA P:107 , ILE P:108 , HOH P:300BINDING SITE FOR RESIDUE SO4 P 206
5AC5SOFTWAREHIS P:144 , ARG P:186 , HOH P:346 , HOH P:354BINDING SITE FOR RESIDUE SO4 P 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SW8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe P:36 -Pro P:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SW8)

(-) Exons   (0, 0)

(no "Exon" information available for 3SW8)

(-) 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 P from PDB  Type:PROTEIN  Length:194
 aligned with Q939R9_STREE | Q939R9 from UniProtKB/TrEMBL  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  
         Q939R9_STREE     2 SAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE 203
               SCOP domains d3sw8p_ P: Peptide deformylase                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh......hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeeee..--------..eeeeeeeeeeeeeee...eeee..................ee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh...........eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sw8 P   2 SAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNI--------EAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLILE 203
                                    11        21        31        41        51        61        71        81        91|      101       111       121       131       141       151       161       171       181       191       201  
                                                                                                                     92      101
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 3SW8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SW8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (Q939R9_STREE | Q939R9)
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: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
        Q939R9_STREE | Q939R9: 3svj
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(-) Related Entries Specified in the PDB File

3str 3svj