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(-) Description

Title :  CRYSTAL STRUCTURE OF S.AUREUS PEPTIDE DEFORMYLASE
 
Authors :  V. Mikol
Date :  14 May 02  (Deposition) - 24 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pdf, Peptide 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 PDF1
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:65 , CYS B:111 , HIS B:154 , HIS B:158 , HOH B:208 , HOH B:236BINDING SITE FOR RESIDUE ZN B 201
2AC2SOFTWAREGLN A:65 , CYS A:111 , HIS A:154 , HIS A:158 , HOH A:220BINDING SITE FOR RESIDUE ZN A 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:24 -Pro A:25
2Leu B:24 -Pro B:25

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LQW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1LQW)

(-) Sequences/Alignments

Asymmetric 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:183
 aligned with DEF_STAAU | P68826 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
            DEF_STAAU     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
               SCOP domains d1lqwa_ A: Peptide deformylase                                                                                                                                                          SCOP domains
               CATH domains 1lqwA00 A:1-183 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeeee....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqw A   1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with DEF_STAAU | P68826 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
            DEF_STAAU     1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
               SCOP domains d1lqwb_ B: Peptide deformylase                                                                                                                                                          SCOP domains
               CATH domains 1lqwB00 B:1-183 Peptide Deformylase                                                                                                                                                     CATH domains
           Pfam domains (1) ---Pep_deformylase-1lqwB01 B:4-174                                                                                                                                            --------- Pfam domains (1)
           Pfam domains (2) ---Pep_deformylase-1lqwB02 B:4-174                                                                                                                                            --------- Pfam domains (2)
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhh............ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lqw B   1 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_STAAU | P68826: 1lm4 1lmh 1q1y 2ai9

(-) Related Entries Specified in the PDB File

1lqy 1LQY IS THE CRYSTAL STRUCTURE OF B.STEAROTHERMOPHILLUS DEFORMYLASE.
1lru 1LRU IS THE CRYSTAL STRUCTURE OF E.COLI DEFORMYLASE.
1lry 1LRY IS THE CRYSTAL STRUCTURE OF P.AERUGINOSA DEFORMYLASE.