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(-) Description

Title :  STRUCTURE AND ACTIVITY OF HUMAN MITOCHONDRIAL PEPTIDE DEFORMYLASE, A NOVEL CANCER TARGET
 
Authors :  S. Escobar-Alvarez, Y. Goldgur, G. Yang, O. Ouerfelli, Y. Li, D. A. Sche
Date :  05 Feb 09  (Deposition) - 07 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 2:  A (1x),C (1x)
Biol. Unit 3:  B (1x),D (1x)
Keywords :  Peptide Deformylase, Actinonin, Hydrolase, Iron, Metal-Binding, Mitochondrion, Protein Biosynthesis, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Escobar-Alvarez, Y. Goldgur, G. Yang, O. Ouerfelli, Y. Li, D. A. Scheinberg
Structure And Activity Of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target
J. Mol. Biol. V. 387 1211 2009
PubMed-ID: 19236878  |  Reference-DOI: 10.1016/J.JMB.2009.02.032

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE, MITOCHONDRIAL
    Chains: A, B, C, D
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PDF, PDF1A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 2 (1x): A (1x) C (1x) 
Biological Unit 3 (1x):  B (1x) D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BB24Ligand/IonACTINONIN
2CO4Ligand/IonCOBALT (II) ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BB22Ligand/IonACTINONIN
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BB21Ligand/IonACTINONIN
2CO-1Ligand/IonCOBALT (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:50 , VAL A:51 , GLY A:52 , GLN A:57 , PRO A:111 , GLU A:112 , GLY A:113 , CYS A:114 , GLU A:115 , TRP A:149 , ARG A:152 , HIS A:156 , GLU A:157 , HIS A:160 , CO A:1002 , HOH A:1061BINDING SITE FOR RESIDUE BB2 A 1001
2AC2SOFTWARECYS B:50 , VAL B:51 , GLY B:52 , GLN B:57 , ARG B:85 , PRO B:111 , GLU B:112 , GLY B:113 , CYS B:114 , GLU B:115 , TRP B:149 , ARG B:152 , HIS B:156 , GLU B:157 , HIS B:160 , CO B:1003 , HOH B:1069 , HOH B:1085BINDING SITE FOR RESIDUE BB2 B 1002
3AC3SOFTWARECO C:1 , CYS C:50 , VAL C:51 , GLY C:52 , GLN C:57 , ARG C:85 , PRO C:111 , GLU C:112 , GLY C:113 , CYS C:114 , GLU C:115 , LEU C:121 , TRP C:149 , ARG C:152 , HIS C:156 , GLU C:157 , HIS C:160 , HOH C:1065BINDING SITE FOR RESIDUE BB2 C 1003
4AC4SOFTWARECO D:2 , CYS D:50 , VAL D:51 , GLY D:52 , GLN D:57 , PRO D:111 , GLU D:112 , GLY D:113 , CYS D:114 , GLU D:115 , TRP D:149 , HIS D:156 , GLU D:157 , HIS D:160 , HOH D:1117BINDING SITE FOR RESIDUE BB2 D 1004
5AC5SOFTWAREGLN C:57 , CYS C:114 , HIS C:156 , HIS C:160 , BB2 C:1003BINDING SITE FOR RESIDUE CO C 1
6AC6SOFTWAREGLN D:57 , CYS D:114 , HIS D:156 , HIS D:160 , BB2 D:1004BINDING SITE FOR RESIDUE CO D 2
7AC7SOFTWAREGLN A:57 , CYS A:114 , HIS A:156 , HIS A:160 , BB2 A:1001BINDING SITE FOR RESIDUE CO A 1002
8AC8SOFTWAREGLN B:57 , CYS B:114 , HIS B:156 , HIS B:160 , BB2 B:1002BINDING SITE FOR RESIDUE CO B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G5K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G5K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G5K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G5K)

(-) Exons   (0, 0)

(no "Exon" information available for 3G5K)

(-) 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 DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5ka_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          kA00 A:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhhh.hhhhhhhhh...eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5k A   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5kb_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          kB00 B:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeeehhhhhhh.hhhhhhhhh...eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5k B   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5kc_ C: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          kC00 C:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeeehhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5k C   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:183
 aligned with DEFM_HUMAN | Q9HBH1 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:193
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           DEFM_HUMAN    51 HLRRLVLGPPEPPFSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 243
               SCOP domains d3g          5kd_ D: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3g5          kD00 D:3-185 Peptide Deformylase                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...----------........hhhhh......hhhhh.hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeeehhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5k D   3 HMS----------FSHVCQVGDPVLRGVAAPVERAQLGGPELQRLTQRLVQVMRRRRCVGLSAPQLGVPRQVLALELPEALCRECPPRQRALRQMEPFPLRVFVNPSLRVLDSRLVTFPEGCESVAGFLACVPRFQAVQISGLDPNGEQVVWQASGWAARIIQHEMDHLQGCLFIDKMDSRTFTNVYWMKVND 185
                              |      -   |    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182   
                              5          6
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G5K)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DEFM_HUMAN | Q9HBH1)
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:0031365    N-terminal protein amino acid modification    The alteration of the N-terminal amino acid residue in a protein.
    GO:0018206    peptidyl-methionine modification    The modification of peptidyl-methionine.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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        DEFM_HUMAN | Q9HBH1: 3g5p

(-) Related Entries Specified in the PDB File

1g2a 1ix1 1lqw 1zy0 1zy1 3g5p