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(-) Description

Title :  S.AUREUS POLYPEPTIDE DEFORMYLASE
 
Authors :  K. J. Smith, C. M. Petit, K. Aubart, M. Smyth, E. Mcmanus, J. Jones, A. Fosberry, C. Lewis, M. Lonetto, S. B. Christensen
Date :  29 Jul 05  (Deposition) - 06 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hudrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Smith, C. M. Petit, K. Aubart, M. Smyth, E. Mcmanus, J. Jones, A. Fosberry, C. Lewis, M. Lonetto, S. B. Christensen
Structural Variation And Inhibitor Binding In Polypeptide Deformylase From Four Different Bacterial Species.
Protein Sci. V. 12 349 2003
PubMed-ID: 12538898  |  Reference-DOI: 10.1110/PS.0229303
(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 Taxid: 562
    Gene: DEF, DEF1, PDF1
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:110 , HIS B:153 , HIS B:157 , HOH B:3010BINDING SITE FOR RESIDUE NI B 301
2AC2SOFTWAREGLN A:64 , CYS A:110 , HIS A:153 , HIS A:157 , HOH A:322BINDING SITE FOR RESIDUE NI A 302
3AC3SOFTWAREARG A:51 , ARG B:8BINDING SITE FOR RESIDUE SO4 B 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AI9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:23 -Pro A:24
2Leu B:23 -Pro B:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AI9)

(-) Exons   (0, 0)

(no "Exon" information available for 2AI9)

(-) 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 d2ai9a_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains 2ai9A00 A:0-182 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.............ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ai9 A   0 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 182
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   


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 d2ai9b_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains 2ai9B00 B:0-182 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee........eeeeeeeeeeeee...eee...................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh...........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ai9 B   0 MLTMKDIIRDGHPTLRQKAAELELPLTKEEKETLIAMREFLVNSQDEEIAKRYGLRSGVGLAAPQINISKRMIAVLIPDDGSGKSYDYMLVNPKIVSHSVQEAYLPTGEGCLSVDDNVAGLVHRHNRITIKAKDIEGNDIQLRLKGYPAIVFQHEIDHLNGVMFYDHIDKNHPLQPHTDAVEV 182
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AI9)

(-) 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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  2ai9
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2ai7 2ai8 2aia 2aie