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(-) Description

Title :  PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM
 
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 :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydrolase, Iron Metalloprotease; Protein Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Becker, I. Schlichting, W. Kabsch, S. Schultz, A. F. Wagner
Structure Of Peptide Deformylase And Identification Of The Substrate Binding Site.
J. Biol. Chem. V. 273 11413 1998
PubMed-ID: 9565550  |  Reference-DOI: 10.1074/JBC.273.19.11413
(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 NI2+ CONTAINING FORM
    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  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NI3Ligand/IonNICKEL (II) ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:552 , ILE B:553 , HIS B:554 , GLN B:555 , ARG C:1029BINDING SITE FOR RESIDUE SO4 B 3001
2AC2SOFTWAREARG B:529 , ILE C:1053 , HIS C:1054 , GLN C:1055BINDING SITE FOR RESIDUE SO4 B 3002
3AC3SOFTWARECYS A:90 , HIS A:132 , HIS A:136 , HOH A:2034BINDING SITE FOR RESIDUE NI A 2001
4AC4SOFTWAREGLN B:550 , CYS B:590 , HIS B:632 , HIS B:636 , HOH B:3004BINDING SITE FOR RESIDUE NI B 2001
5AC5SOFTWAREGLN C:1050 , CYS C:1090 , HIS C:1132 , HIS C:1136 , HOH C:3005BINDING SITE FOR RESIDUE NI C 2001
6NIAAUTHORCYS A:90 , HIS A:132 , HIS A:136NI BINDING SITE FOR CHAIN A
7NIBAUTHORCYS B:590 , HIS B:632 , HIS B:636NI BINDING SITE FOR CHAIN B
8NICAUTHORCYS C:1090 , HIS C:1132 , HIS C:1136NI BINDING SITE FOR CHAIN C

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BS7)

(-) 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 1BS7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BS7)

(-) Exons   (0, 0)

(no "Exon" information available for 1BS7)

(-) 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 d1bs7a_ A: Peptide deformylase                                                                                                                                           SCOP domains
               CATH domains 1bs7A00 A:1-168 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
                1bs7 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 d1bs7b_ B: Peptide deformylase                                                                                                                                           SCOP domains
               CATH domains 1bs7B00 B:501-668 Peptide Deformylase                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhh..........hhhhhhhhhhhhhhhhh...eeehhhh.....eeee.........eeee..eeeeee.......................eeeeeee.....eeeeeeehhhhhhhhhhhhhhh...hhhh..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bs7 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 d1bs7c_ C: Peptide deformylase                                                                                                                                           SCOP domains
               CATH domains 1bs7C00 C:1001-1168 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhh..........hhhhhhhhhhhhhhhhh...eeehhhh.....eeee.........eeee..eeeeee.......................eeeeeee.....eeeeeeehhhhhhhhhhhhhhh...hhhh..hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1bs7 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 1BS7)

(-) 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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  1bs7
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_ECOLI | P0A6K3: 1bs4 1bs5 1bs6 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

1bs4 1bs5 1bs6 1bs8 1bsz