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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS PEPTIDE DEFORMYLASE COMPLEXED WITH ANTIBIOTIC ACTINONIN
 
Authors :  M. Mathieu, V. Mikol
Date :  14 May 02  (Deposition) - 24 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Actinonin, Inhibition, Polypeptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Guilloteau, M. Mathieu, C. Giglione, V. Blanc, A. Dupuy, M. Chevrier, P. Gil, A. Famechon, T. Meinnel, V. Mikol
The Crystal Structures Of Four Peptide Deformylases Bound To The Antibiotic Actinonin Reveal Two Distinct Types: A Platform For The Structure-Based Design Of Antibacterial Agents.
J. Mol. Biol. V. 320 951 2002
PubMed-ID: 12126617  |  Reference-DOI: 10.1016/S0022-2836(02)00549-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE 2
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: PDF 2, POLYPEPTIDE DEFORMYLASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2NI2Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , CYS A:110 , HIS A:153 , HIS A:157 , BB2 A:401BINDING SITE FOR RESIDUE NI A 301
2AC2SOFTWAREHIS A:97 , HOH A:485 , HOH A:549 , HOH A:555 , HOH A:617BINDING SITE FOR RESIDUE NI A 302
3AC3SOFTWARELYS A:5 , PRO A:57 , GLY A:58 , ILE A:59 , GLY A:60 , GLN A:65 , LEU A:104 , THR A:106 , GLY A:107 , GLY A:109 , CYS A:110 , LEU A:111 , HIS A:153 , GLU A:154 , HIS A:157 , NI A:301 , HOH A:435BINDING SITE FOR RESIDUE BB2 A 401

(-) SS Bonds  (0, 0)

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

(-) 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 1LQY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LQY)

(-) 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:184
 aligned with DEF2_GEOSE | O31410 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
           DEF2_GEOSE     1 MITMKDIIKEGHPTLRKVAEPVPLPPSEEDKRILQSLLDYVKMSQDPELAAKYGLRPGIGLAAPQINVSKRMIAVHVTDENGTLYSYALFNPKIVSHSVQQCYLTTGEGCLSVDRDVPGYVLRYARITVTGTTLDGEEVTLRLKGLPAIVFQHEIDHLNGIMFYDRINPADPFQVPDGAIPIGR 184
               SCOP domains d1lqya_ A: Peptide deformylase                                                                                                                                                           SCOP domains
               CATH domains 1lqyA00 A:1-184 Peptide Deformylase                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeeee.....eeeeeeeeeeeeee...eeee..................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqy A   1 MITMKDIIKEGHPTLRKVAEPVPLPPSEEDKRILQSLLDYVKMSQDPELAAKYGLRPGIGLAAPQINVSKRMIAVHVTDENGTLYSYALFNPKIVSHSVQQCYLTTGEGCLSVDRDVPGYVLRYARITVTGTTLDGEEVTLRLKGLPAIVFQHEIDHLNGIMFYDRINPADPFQVPDGAIPIGR 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
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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 1LQY)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DEF2_GEOSE | O31410)
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)

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(-) Related Entries Specified in the PDB File

1lqw 1LQW IS THE CRYSTAL STRUCTURE OF S.AUREUS PEPTIDE DEFORMYLASE.
1lru 1LRU IS THE CRYSTAL STRUCTURE OF E.COLI DEFORMYLASE.
1lry 1LRY IS THE CRYSTAL STRUCTURE OF P.AERUGINOSA DEFORMYLASE.