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(-) Description

Title :  CRYSTAL STRUCTURES OF PEPTIDE DEFORMYLASE FROM STAPHYLOCOCCUS AUREUS COMPLEXED WITH ACTINONIN
 
Authors :  H. J. Yoon, S. K. Lee, H. L. Kim, H. W. Kim, H. W. Kim, J. Y. Lee, B. Mikami, S.
Date :  23 Jul 03  (Deposition) - 23 Jul 04  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Metallo-Enzyme, Peptide Deformylase, Actinonin, Staphylococcus Aureus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Yoon, H. L. Kim, S. K. Lee, H. W. Kim, H. W. Kim, J. Y. Lee, B. Mikami, S. W. Suh
Crystal Structure Of Peptide Deformylase From Staphylococcu Aureus In Complex With Actinonin, A Naturally Occurring Antibacterial Agent
Proteins V. 57 639 2004
PubMed-ID: 15382235  |  Reference-DOI: 10.1002/PROT.20231

(-) 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: SA113
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SA1100
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: PDF

 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
1BB21Ligand/IonACTINONIN
2CSD1Mod. Amino Acid3-SULFINOALANINE
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , CSD A:111 , HIS A:154 , HIS A:158 , BB2 A:301BINDING SITE FOR RESIDUE ZN A 350
2AC2SOFTWAREARG A:56 , SER A:57 , GLY A:58 , VAL A:59 , GLY A:60 , GLN A:65 , LEU A:105 , GLU A:109 , GLY A:110 , CSD A:111 , LEU A:112 , ILE A:150 , VAL A:151 , HIS A:154 , GLU A:155 , HIS A:158 , GLU A:185 , ZN A:350 , HOH A:611BINDING SITE FOR RESIDUE BB2 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q1Y)

(-) 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 1Q1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q1Y)

(-) 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:186
 aligned with DEF_STAAU | P68826 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:186
                                                                                                                                                                                                                183   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  |   
            DEF_STAAU     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV---   -
               SCOP domains d1q1ya_ A: Peptide deformylase                                                                                                                                                             SCOP domains
               CATH domains 1q1yA00 A:1-186 Peptide Deformylase                                                                                                                                                        CATH domains
               Pfam domains ---Pep_deformylase-1q1yA01 A:4-174                                                                                                                                            ------------ 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
                 1q1y A   1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGcLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKDHPLQPHTDAVEVLEH 186
                                    10        20        30        40        50        60        70        80        90       100       110|      120       130       140       150       160       170       180      
                                                                                                                                        111-CSD
   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  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEF_STAAU | P68826)
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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  1q1y
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_STAAU | P68826: 1lm4 1lmh 1lqw 2ai9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Q1Y)