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(-) Description

Title :  CRYSTAL STRUCTURE OF P.AERUGINOSA PEPTIDE DEFORMYLASE COMPLEXED WITH ANTIBIOTIC ACTINONIN
 
Authors :  H. -W. Kim, H. -J. Yoon, J. Y. Lee, B. W. Han, J. K. Yang, B. I. Lee, H. J. Ahn, H. H. Lee, S. W. Suh
Date :  07 Jun 02  (Deposition) - 09 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Inhibitor Complex, 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 Staphylococcus Aureus In Complex With Actinonin, A Naturally Occurring Antibacterial Agent
Proteins V. 57 639 2004
PubMed-ID: 15382235  |  Reference-DOI: 10.1002/PROT.20231
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1BB22Ligand/IonACTINONIN
2MHA2Ligand/Ion(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:92 , HIS A:134 , HIS A:138 , BB2 A:1301BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREGLN B:51 , CYS B:92 , HIS B:134 , HIS B:138 , BB2 B:2301BINDING SITE FOR RESIDUE ZN B 201
3AC3SOFTWAREASP A:25 , ASP A:26 , GLY A:44 , ILE A:45 , GLY A:46 , GLN A:51 , TYR A:88 , GLN A:89 , GLU A:90 , GLY A:91 , CYS A:92 , LEU A:93 , TYR A:99 , HIS A:134 , GLU A:135 , HIS A:138 , ZN A:201 , HOH A:1344BINDING SITE FOR RESIDUE BB2 A 1301
4AC4SOFTWAREARG A:71 , VAL A:72 , PHE A:73 , ASP A:114 , ARG A:115 , PHE A:120 , GLU A:122 , HOH A:1336 , HOH A:1452 , ARG B:109 , GLU B:121BINDING SITE FOR RESIDUE MHA A 401
5AC5SOFTWAREGLY B:44 , ILE B:45 , GLY B:46 , GLN B:51 , TYR B:88 , GLN B:89 , GLU B:90 , GLY B:91 , CYS B:92 , LEU B:93 , TYR B:99 , HIS B:134 , GLU B:135 , HIS B:138 , ZN B:201 , HOH B:2430BINDING SITE FOR RESIDUE BB2 B 2301
6AC6SOFTWARELYS A:107 , ARG A:109 , VAL A:123 , ARG B:71 , VAL B:72 , PHE B:73 , ASP B:114 , ARG B:115 , PHE B:120 , GLU B:122 , HOH B:2333BINDING SITE FOR RESIDUE MHA B 1401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IX1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:9 -Pro A:10
2Ala A:42 -Pro A:43
3Phe B:9 -Pro B:10
4Ala B:42 -Pro B:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IX1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IX1)

(-) Exons   (0, 0)

(no "Exon" information available for 1IX1)

(-) 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:169
 aligned with DEF_PSEAE | Q9I7A8 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:169
                                                                                                                                                                                                168  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |  
            DEF_PSEAE     2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQA--   -
               SCOP domains d1ix1a_ A: Peptide deformylase                                                                                                                                            SCOP domains
               CATH domains 1ix1A00 A:2-170 Peptide Deformylase                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeee....eeeeee.........eeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ix1 A   2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQAHH 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         


Chain B from PDB  Type:PROTEIN  Length:169
 aligned with DEF_PSEAE | Q9I7A8 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:169
                                                                                                                                                                                                168  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |  
            DEF_PSEAE     2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQA--   -
               SCOP domains d1ix1b_ B: Peptide deformylase                                                                                                                                            SCOP domains
               CATH domains 1ix1B00 B:2-170 Peptide Deformylase                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ix1 B   2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQAHH 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IX1)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DEF_PSEAE | Q9I7A8)
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:0031365    N-terminal protein amino acid modification    The alteration of the N-terminal amino acid residue in a protein.
    GO:0043686    co-translational protein modification    The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
    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_PSEAE | Q9I7A8: 1lry 1n5n 1s17

(-) Related Entries Specified in the PDB File

1bs4 1BS4 CONTAINS PEPTIDE DEFORMYLAS AS ZN2+ CONTAINING FORM (NATIVE) COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL