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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  A. Kreusch, G. Spraggon, C. C. Lee, H. Klock, D. Mcmullan, K. Ng, T. Shin, J. Vincent, I. Warner, C. Ericson, S. A. Lesley
Date :  30 Apr 02  (Deposition) - 24 Jun 03  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Pdf, Metalloenzyme, Peptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kreusch, G. Spraggon, C. C. Lee, H. Klock, D. Mcmullan, K. Ng, T. Shin J. Vincent, I. Warner, C. Ericson, S. A. Lesley
Structure Analysis Of Peptide Deformylases From Streptococcus Pneumoniae, Staphylococcus Aureus, Thermotoga Maritima, And Pseudomonas Aeruginosa: Snapshots Of The Oxygen Sensitivity Of Peptide Deformylase
J. Mol. Biol. V. 330 309 2003
PubMed-ID: 12823970  |  Reference-DOI: 10.1016/S0022-2836(03)00596-5

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE DEFB
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313

 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
1FE1Ligand/IonFE (III) ION
2GOL1Ligand/IonGLYCEROL
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:77 , OCS A:130 , HIS A:173 , HIS A:177 , HOH A:369BINDING SITE FOR RESIDUE FE A 204
2AC2SOFTWAREGLU A:128 , GLY A:129 , TYR A:166 , HIS A:173 , HOH A:409BINDING SITE FOR RESIDUE GOL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LM6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:36 -Pro A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LM6)

(-) Exons   (0, 0)

(no "Exon" information available for 1LM6)

(-) 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:191
 aligned with DEF_STRPN | Q9F2F0 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
            DEF_STRPN     1 MSAIERITKAAHLIDMNDIIREGNPTLRAIAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPNIVEEGETPQEAYDLEAIMYNPKIVSHSVQDAALGEGEGCLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLIL 202
               SCOP domains d1lm6a_ A: Peptide deformylase                                                                                                                                                                             SCOP domains
               CATH domains 1lm6A00 A:1-202 Peptide Deformylase                                                                                                                                                                        CATH domains
               Pfam domains ---------------Pep_deformylase-1lm6A01 A:16-193                                                                                                                                                  --------- Pfam domains
         Sec.struct. author .hhhhhhh......hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeee..-----------..eeeeeeeeeeeee...eeee..................ee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh...........eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lm6 A   1 MSAIERITKAAHLIDMNDIIREGNPTLRTVAEEVTFPLSDQEIILGEKMMQFLKHSQDPVMAEKMGLRGGVGLAAPQLDISKRIIAVLVPN-----------YDLEAIMYNPKIVSHSVQDAALGEGEGcLSVDRNVPGYVVRHARVTVDYFDKDGEKHRIKLKGYNSIVVQHEIDHINGIMFYDRINEKDPFAVKDGLLIL 202
                                    10        20        30        40        50        60        70        80        90|        -  |    110       120       130       140       150       160       170       180       190       200  
                                                                                                                     91         103                        130-OCS
   Legend:   → Mismatch (orange background)
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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_STRPN | Q9F2F0)
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

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(-) Related Entries Specified in the PDB File

1lm4 1LM4 IS THE PDF STRUCTURE FROM STAPHYLOCOCCUS AUREUS
1lme 1LME IS THE PDF STRUCTURE FROM THERMOTOGA MARITIMA