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(-) Description

Title :  CRYSTAL STRUCTURE OF AN EFPDF COMPLEX WITH MET-ALA-SER
 
Authors :  K. Y. Hwang, K. H. Nam
Date :  07 Feb 09  (Deposition) - 03 Mar 09  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,F,G
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,G  (1x)
Keywords :  Pdf, Peptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Nam, K. H. Kim, E. E. Kim, K. Y. Hwang
Crystal Structure Of An Efpdf Complex With Met-Ala-Ser Based On Crystallographic Packing.
Biochem. Biophys. Res. Commun. V. 381 630 2009
PubMed-ID: 19249287  |  Reference-DOI: 10.1016/J.BBRC.2009.02.113
(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: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352
 
Molecule 2 - PEPTIDE (MET)(ALA)(SER)
    Chains: F, G
    Engineered: YES
    Other Details: THIS IS TRIPEPTIDE. THE AUTHOR PURCHASED FROM SIGAM COMPANY
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFG
Biological Unit 1 (1x): A F 
Biological Unit 2 (1x):  B G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2NA5Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , CYS A:114 , HIS A:157 , HIS A:161 , HOH A:231BINDING SITE FOR RESIDUE FE A 188
2AC2SOFTWAREHOH A:257BINDING SITE FOR RESIDUE NA A 189
3AC3SOFTWAREGLN B:65 , CYS B:114 , HIS B:157 , HIS B:161 , HOH B:247BINDING SITE FOR RESIDUE FE B 188
4AC4SOFTWARESER B:23 , ASP B:30BINDING SITE FOR RESIDUE NA B 189
5AC5SOFTWAREGLU B:181BINDING SITE FOR RESIDUE NA B 190
6AC6SOFTWAREGLU B:10 , ARG B:16 , TYR B:168BINDING SITE FOR RESIDUE NA B 191
7AC7SOFTWARESER B:100 , HIS B:101 , SER B:102 , ARG B:146BINDING SITE FOR RESIDUE NA B 192

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G6N)

(-) 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 3G6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G6N)

(-) Exons   (0, 0)

(no "Exon" information available for 3G6N)

(-) 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 Q842S4_ENTFC | Q842S4 from UniProtKB/TrEMBL  Length:187

    Alignment length:191
                                1                                                                                                                                                                                          
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186 
         Q842S4_ENTFC     - ----MITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPSPDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g6nA00 A:-3-187 Peptide Deformylase                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee..--------.eeeeeeeeeeeee...eeee..................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g6n A  -3 GSHMMITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPS--------SLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
                                     6        16        26        36        46        56        66        76  |      - |      96       106       116       126       136       146       156       166       176       186 
                                                                                                             79       88                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with Q842S4_ENTFC | Q842S4 from UniProtKB/TrEMBL  Length:187

    Alignment length:191
                                1                                                                                                                                                                                          
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186 
         Q842S4_ENTFC     - ----MITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPSPDPEADGPSLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g6nB00 B:-3-187 Peptide Deformylase                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh......eee.hhhh....eeeeee..--------.eeeeeeeeeeeee...eeee..................ee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g6n B  -3 GSHMMITMDDIIREGNPTLREVAKEVSLPLSEEDISLGKEMLEFLKNSQDPIKAEELHLRGGVGLAAPQLDISKRIIAVHVPS--------SLSTVMYNPKILSHSVQDACLGEGEGCLSVDREVPGYVVRHAKITVSYYDMNGEKHKIRLKNYESIVVQHEIDHINGVMFYDHINDQNPFALKEGVLVIE 187
                                     6        16        26        36        46        56        66        76  |      - |      96       106       116       126       136       146       156       166       176       186 
                                                                                                             79       88                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3g6n F   1 MAS   3


Chain G from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 3g6n G   1 MAS   3
   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  (0, 0)

(no "SCOP Domain" information available for 3G6N)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G6N)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q842S4_ENTFC | Q842S4)
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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        Q842S4_ENTFC | Q842S4: 3cmd

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3cmd NATIVE STRUCTURE