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(-) Description

Title :  CRYSTAL STRUCTURES OF THE STAPHYLOCOCCUS AUREUS PEPTIDE DEFORMYLASE IN COMPLEX WITH TWO CLASSES OF NEW INHIBITORS
 
Authors :  S. J. Lee, S. -J. Lee, S. K. Lee, H. -J. Yoon, H. H. Lee, K. K. Kim, B. J. Lee, S
Date :  14 Oct 11  (Deposition) - 27 Jun 12  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdf-Inhibitor, Pdf, Peptide Deformylase, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Lee, S. -J. Lee, S. K. Lee, H. -J. Yoon, H. H. Lee, K. K. Kim, B. J. Lee, B. I. Lee, S. W. Suh
Structures Of Staphylococcus Aureus Peptide Deformylase In Complex With Two Classes Of New Inhibitors
Acta Crystallogr. , Sect. D V. 68 784 2012
PubMed-ID: 22751663  |  Reference-DOI: 10.1107/S0907444912011912

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SACOL1100
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL
    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
1CSD1Mod. Amino Acid3-SULFINOALANINE
2MDB1Ligand/Ion(S)-N-(CYCLOPENTYLMETHYL)-N-(2-(HYDROXYAMINO)-2-OXOETHYL)-2-(3-(2-METHOXYPHENYL)UREIDO)-3,3-DIMETHYLBUTANAMIDE
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:45 , ARG A:56 , SER A:57 , GLY A:58 , VAL A:59 , GLY A:60 , GLN A:65 , GLU A:109 , GLY A:110 , CSD A:111 , LEU A:112 , TYR A:147 , HIS A:154 , GLU A:155 , HIS A:158 , GLU A:185 , HOH A:196 , HOH A:246 , ZN A:350BINDING SITE FOR RESIDUE MDB A 301
2AC2SOFTWAREGLN A:65 , CSD A:111 , HIS A:154 , HIS A:158 , MDB A:301BINDING SITE FOR RESIDUE ZN A 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U7K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:24 -Pro A:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U7K)

(-) Exons   (0, 0)

(no "Exon" information available for 3U7K)

(-) 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:185
 aligned with DEF_STAAC | Q5HGZ3 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:185
                                                                                                                                                                                                                183  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  |  
            DEF_STAAC     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKDHPLQPHTDAVEV--   -
               SCOP domains d3u7ka_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u7k A   1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGcLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKDHPLQPHTDAVEVLE 185
                                    10        20        30        40        50        60        70        80        90       100       110|      120       130       140       150       160       170       180     
                                                                                                                                        111-CSD
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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 3U7K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U7K)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEF_STAAC | Q5HGZ3)
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
        DEF_STAAC | Q5HGZ3: 3u7l 3u7m 3u7n

(-) Related Entries Specified in the PDB File

3u7l 3u7m 3u7n