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(-) Description

Title :  PEPTIDE DEFORMYLASE AS ZN2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL
 
Authors :  A. Becker, I. Schlichting, W. Kabsch, D. Groche, S. Schultz, A. F. V. Wagner
Date :  01 Sep 98  (Deposition) - 27 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Complex(Enzyme/Inhibitor), Hydrolase, Iron Metalloprotease, Protein Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Becker, I. Schlichting, W. Kabsch, D. Groche, S. Schultz, A. F. Wagner
Iron Center, Substrate Recognition And Mechanism Of Peptide Deformylase.
Nat. Struct. Biol. V. 5 1053 1998
PubMed-ID: 9846875  |  Reference-DOI: 10.1038/4162
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PEPTIDE DEFORMYLASE)
    Cellular Location: CYTOPLASMA
    Chains: A, B, C
    EC Number: 3.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: DEF
    Expression System Plasmid: P925C
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector: PKK223-3 (PHARMACIA)
    Expression System Vector Type: PLASMID
    Gene: DEF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: PDF PROTEIN FROM ESCHERICHIA COLI IS CRYSTALLIZED AS ZN2+ CONTAINING FORM, COCRYSTALLIZED WITH INHIBITOR POLYETHYLENE GLYCOL (PEG)
    Strain: JM109
    Synonym: PDF

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
12PE3Ligand/IonNONAETHYLENE GLYCOL
2SO42Ligand/IonSULFATE ION
3ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2SO4-1Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:518 , HIS B:554 , GLN B:555 , HOH B:2064 , ARG C:1029BINDING SITE FOR RESIDUE SO4 B 3001
02AC2SOFTWAREARG B:529 , HOH C:137 , ILE C:1053 , HIS C:1054 , GLN C:1055BINDING SITE FOR RESIDUE SO4 C 3002
03AC3SOFTWAREGLN A:50 , CYS A:90 , HIS A:132 , HIS A:136 , HOH A:8068BINDING SITE FOR RESIDUE ZN A 2001
04AC4SOFTWARECYS B:590 , HIS B:632 , HIS B:636 , HOH B:9254BINDING SITE FOR RESIDUE ZN B 2002
05AC5SOFTWARECYS C:1090 , HIS C:1132 , HIS C:1136 , HOH C:9255BINDING SITE FOR RESIDUE ZN C 2003
06AC6SOFTWAREGLU A:41 , GLU A:42 , GLY A:43 , ILE A:44 , GLY A:45 , GLU A:88 , GLY A:89 , LEU A:91 , PRO A:94 , GLU A:95 , ARG A:97 , HIS A:132 , GLU A:133 , LEU B:649BINDING SITE FOR RESIDUE 2PE A 170
07AC7SOFTWAREGLU B:541 , GLU B:542 , GLY B:543 , ILE B:544 , GLU B:587 , GLY B:589 , LEU B:591 , ARG B:597 , CYS B:629 , GLU B:633 , HOH B:9094 , LYS C:1018BINDING SITE FOR RESIDUE 2PE B 2
08AC8SOFTWAREHOH C:210 , GLU C:1042 , GLY C:1043 , ILE C:1044 , GLY C:1045 , GLU C:1087 , GLU C:1088 , GLY C:1089 , CYS C:1090 , LEU C:1091 , PRO C:1094 , GLU C:1095 , ARG C:1097 , CYS C:1129 , HIS C:1132 , GLU C:1133BINDING SITE FOR RESIDUE 2PE C 3
09ZNAAUTHORCYS A:90 , HIS A:132 , HIS A:136ONE PEG MOLECULE IS LOCATED IN ACTIVE SITE NEAR ZINC ION
10ZNBAUTHORCYS B:590 , HIS B:632 , HIS B:636ONE PEG MOLECULE IS LOCATED IN ACTIVE SITE NEAR ZINC ION
11ZNCAUTHORCYS C:1090 , HIS C:1132 , HIS C:1136ONE PEG MOLECULE IS LOCATED IN ACTIVE SITE NEAR ZINC ION

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BS4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:8 -Pro A:9
2Ile B:508 -Pro B:509
3Ile C:1008 -Pro C:1009

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BS4)

(-) Exons   (0, 0)

(no "Exon" information available for 1BS4)

(-) 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:168
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           DEF_ECOLI      2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA  169
               SCOP domains d1bs4a_ A: Peptide deformylase                                                                                                                                           SCOP domains
               CATH domains 1bs4A00 A:1-168 Peptide Deformylase                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhh..........hhhhhhhhhhhhhhhh....eeehhhh.....eeee.........eeee..eeeeee.......................eeeeeee.....eeeeeeehhhhhhhhhhhhhhh...hhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bs4 A    1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA  168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           DEF_ECOLI      2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA  169
               SCOP domains d1bs4b_ B: Peptide deformylase                                                                                                                                           SCOP domains
               CATH domains 1bs4B00 B:501-668 Peptide Deformylase                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhh..........hhhhhhhhhhhhhhhh....eeehhhh.....eeee.........eeee..eeeeee..eeeee.........eeeee..eeeeeee.....eeeeee.hhhhhhhhhhhhhhh...hhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bs4 B  501 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA  668
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660        


Chain C from PDB  Type:PROTEIN  Length:168
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           DEF_ECOLI      2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA  169
               SCOP domains d1bs4c_ C: Peptide deformylase                                                                                                                                           SCOP domains
               CATH domains 1bs4C00 C:1001-1168 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhh..........hhhhhhhhhhhhhhhhh...eeehhhh.....eeee.........eeee..eeeeee.......................eeeeeee.....eeeeeeehhhhhhhhhhhhhhh...hhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bs4 C 1001 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA 1168
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BS4)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (DEF_ECOLI | P0A6K3)
molecular function
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1bs4
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_ECOLI | P0A6K3: 1bs5 1bs6 1bs7 1bs8 1bsj 1bsk 1bsz 1def 1dff 1dtf 1g27 1g2a 1icj 1lru 1xem 1xen 1xeo 2ai8 2def 2dtf 2kmn 2w3t 2w3u 3k6l 4al2 4al3 4az4 4v5b

(-) Related Entries Specified in the PDB File

1bs5 1bs6 1bs7 1bs8 1bsz